Medical affairs silos: a case study in strategic misalignment

Here is the contradiction that should keep every Medical Affairs director slightly uncomfortable: 78% of Medical Affairs leaders report greater transparency with Commercial than they did five or ten years ago, while 60% of underperforming pharma sales teams still identify poor cross-functional collaboration as a primary obstacle to performance.

Those figures do not need to come from the same companies to expose the same weakness. One measures how collaboration feels inside the organization. The other reflects what happens when that collaboration reaches the field. The first can improve while the second remains stubbornly poor. That is the uncomfortable gap between perceived alignment and operational alignment.

The biopharma industry has become very good at displaying the appearance of partnership. There are joint planning meetings, shared slide decks, cross-functional committees, and increasingly sophisticated dashboards. Yet an HCP can still receive several contacts from the same company in a short period, each involving a different function and each presenting a slightly different version of the company’s priorities. No single interaction is necessarily inappropriate. Taken together, they can make the organization look uncoordinated.

That is where medical affairs cross-functional collaboration failures become visible. Not in the meeting room, where everyone agrees that alignment matters, but in the external experience created by the organization’s internal structure.

This is not another sermon about breaking down silos. It is a closer look at why siloed Medical Affairs teams continue to operate in parallel, where the structural misalignment actually lives, and what a more disciplined model of collaboration needs to address.

The anatomy of strategic misalignment: why silos persist despite the optics

The positive collaboration statistic should not be dismissed. If Medical Affairs leaders report more transparency with Commercial than in the past, that likely reflects a real change in organizational behavior. The problem is that transparency is not the same as integration.

Teams can share information without sharing a plan. They can attend the same meeting without using the same definition of success. They can approve the same presentation while working to different timelines and protecting different forms of value.

Silos persist for several structural reasons.

• Incentive asymmetry. Medical Affairs is concerned with scientific exchange, evidence generation, stakeholder relationships, publication quality, and the appropriate interpretation of uncertainty. Commercial is concerned with business performance, market dynamics, customer uptake, and the execution of a brand strategy. These priorities are not inherently incompatible. They become incompatible when the organization asks both functions to make decisions without clarifying how their objectives fit together.
• Different reporting architecture. Medical Affairs may sit within a medical or research structure, while Commercial may report through a general manager or commercial leadership. That arrangement is not a flaw in itself. The problem appears when the two functions have no effective governance mechanism above the brand level. In that situation, collaboration depends on personal relationships and local diplomacy rather than on a repeatable operating model.
• Different definitions of evidence. For Medical Affairs, evidence is not simply a persuasive asset. Its provenance, limitations, context, and interpretation matter. Commercial teams may need to translate the same evidence into a clear market proposition. If the translation is not handled carefully, Medical Affairs can feel that scientific nuance is being compressed, while Commercial can feel that the medical function is making useful evidence impossible to use.
• Different decision speeds. A commercial team may need to make a decision within a planning cycle or in response to a competitor. Medical Affairs may be waiting for an evidence-generation milestone, an advisory discussion, a publication process, or a clearer understanding of the clinical question. Treating the slower process as resistance, or the faster process as recklessness, turns a timing difference into a conflict of intent.
• Fragmented information systems. Field medical, sales, medical information, market access, and brand teams may each record stakeholder interactions in different systems or under different rules. Even when data can technically be reconciled, there may be no clear owner responsible for turning that information into a coordinated engagement plan.

The result is what might be called alignment theatre: the appearance of partnership, the production of joint materials, and the regular scheduling of cross-functional meetings without the underlying architecture that would make the partnership work.

Alignment is not a meeting cadence. It is a shared definition of what the organization is trying to move, by when, and how it will know that it has moved it.

The distinction matters because a meeting is an event, while alignment is a property of the operating model. One can be counted on a calendar. The other is visible in decisions, handoffs, stakeholder experience, and the consistency of the organization’s external behavior.

Why goodwill is not enough

The usual response to misalignment is to ask people to collaborate more effectively. That sounds reasonable, but it places the burden on individual behavior while leaving the system unchanged.

A highly cooperative MSL cannot compensate for a fragmented stakeholder database. A thoughtful brand lead cannot resolve reporting-line ambiguity alone. A Commercial leader who wants a strong scientific partnership still needs a governance model that makes the partnership practical when priorities collide.

This is why internal stakeholder conflict resolution in pharma cannot be reduced to better interpersonal skills. Trust matters, but trust develops faster when people know who decides, which evidence is relevant, what information can be shared, and how disagreements are escalated. The operating model creates the conditions in which trust either grows or gets exhausted.

Bridging the planning horizon gap: annual budgets versus multi-year scientific strategy

One of the most persistent causes of misalignment between Commercial and Medical is the planning horizon.

Commercial planning is usually organized around an annual business cycle, with periodic reviews and adjustments as performance, competition, and market conditions change. Medical Affairs planning often needs to account for longer sequences: stakeholder relationship development, evidence generation, investigator engagement, publication activity, data interpretation, and the time required to establish credibility around a scientific question.

Neither approach is unreasonable. The problem is created when one planning process is treated as the real plan and the other is added later as a supporting document.

The mismatch can be summarized in practical terms:

The table is not a claim that every Commercial or Medical Affairs team operates in the same way. It is a reminder that the functions are often evaluated through different clocks.

A commercial plan may be revised when new market information appears. A scientific program may not be capable of being revised at the same speed without compromising its purpose. A publication plan cannot be accelerated simply because a quarterly review has changed. An investigator relationship cannot be treated as an interchangeable channel. An external stakeholder may remember the quality and consistency of an interaction long after an internal team has moved on to another priority.

This is where siloed Medical Affairs teams can appear inflexible. In reality, they may be protecting dependencies that are invisible in a short-cycle business review. But Medical Affairs can also use the long-term nature of science as a shield against legitimate requests for prioritization and accountability. The answer is not to give one function control over the other. It is to make the dependencies explicit.

A more integrated planning process should answer at least five questions:

1. Which scientific questions are important to the asset and to the relevant stakeholders?

2. Which questions can be addressed with existing evidence, and which require further work?

3. Which activities depend on decisions made by Commercial, Market Access, Regulatory, or other functions?

4. What must be known before a major business or launch decision can be made?

5. Where are the points at which the plan should be reviewed, changed, or stopped?

That last question is often missing. Long-term planning does not mean allowing every initiative to continue indefinitely. It means defining how the organization will recognize that an activity is no longer answering an important question or serving a legitimate strategic purpose.

Put the plans in the same room

The practical correction is straightforward, even if it is not easy: Medical Affairs and Commercial plans should be reviewed together, early enough for each function to influence the other.

Medical Affairs should not be asked to retrofit a scientific program after a brand strategy has already been finalized. Commercial should not be expected to infer the business implications of a medical plan from a list of activities. The shared discussion needs to focus on dependencies rather than on the symbolic presence of both functions.

For example, a cross-functional review might examine:

• the scientific questions that are likely to shape stakeholder understanding;
• the evidence available now and the evidence that will mature later;
• the stakeholder groups affected by uncertainty or changes in the evidence base;
• the external engagements that need coordination;
• the decisions that require medical, commercial, regulatory, or access input;
• the assumptions that could invalidate the plan.

This changes the conversation from ownership to sequencing. The point is not to make Medical Affairs the owner of Commercial strategy, or Commercial the owner of Medical Affairs activity. The point is to prevent each function from discovering the other’s priorities only after decisions have become expensive to change.

Operational fragmentation: the cost of uncoordinated stakeholder outreach

Strategic misalignment becomes tangible when an external stakeholder experiences the consequences of internal fragmentation.

A KOL may be contacted by a sales representative about a brand priority, by an MSL about emerging clinical evidence, and by a medical information team in response to a separate request. These contacts may be appropriate individually. They may also be governed by different processes and recorded in different systems. If nobody has a complete view, the organization cannot judge whether the overall pattern is coherent.

This is not an argument for turning every stakeholder interaction into a centrally controlled campaign. Medical and commercial engagements have different purposes, and functional boundaries remain important. It is an argument for recognizing that the stakeholder experiences one company, not the company’s internal org chart.

The cost of fragmented outreach appears in several forms:

• Stakeholder fatigue. The most valuable experts are often the most heavily approached. When outreach is repetitive, poorly timed, or disconnected from previous conversations, access becomes more difficult.
• Loss of organizational credibility. An HCP may not distinguish between the internal causes of inconsistency. If the company appears unable to coordinate basic information, confidence can decline across the relationship.
• Broken insight loops. Medical and Commercial teams may each hear important observations but fail to combine them. Medical may learn that a clinical question is repeatedly misunderstood, while Commercial sees a market barrier around the same issue. If those signals remain separate, the organization loses the chance to respond intelligently.
• Duplicated effort. Multiple teams may prepare overlapping materials, approach the same stakeholder, or commission activities that answer similar questions. Duplication is not merely an efficiency problem. It can create confusion about which message, evidence source, or objective has priority.
• Compliance and governance exposure. Uncoordinated outreach makes it harder to demonstrate that interactions were appropriately planned, documented, and kept within the relevant functional boundaries. Good intentions do not remove the need for a clear process.
• Poor prioritization. Without a shared view of stakeholder engagement, teams can overinvest in visible relationships while neglecting less visible but strategically important scientific questions or communities.

The most expensive word in pharma is not compliance. It is duplication — paid for twice, in trust and in time.

Coordination without functional collapse

A shared engagement calendar can help, but it should not become a mechanism for Commercial to direct Medical Affairs activity or for Medical Affairs to police every commercial interaction. The purpose is coordination, not functional absorption.

A useful model separates three questions:

1. Who owns the relationship or activity?

Ownership should remain clear and consistent with the purpose of the engagement.

2. Who needs visibility?

Relevant teams should know enough to avoid unnecessary duplication and to understand the broader stakeholder context.

3. Who has decision authority over content and boundaries?

Medical, Commercial, Regulatory, and other functions should retain the authority appropriate to their responsibilities.

This distinction helps resolve a common fear: that collaboration means losing independence. It should not. Medical Affairs needs the independence to protect scientific integrity and appropriate exchange. Commercial needs the authority to execute its business responsibilities. What both functions need is a reliable way to see where their activities intersect.

The basic infrastructure can include a shared stakeholder view, agreed rules for recording interactions, regular reconciliation of planned outreach, and a clear escalation route when two activities may conflict or duplicate one another. None of this replaces judgment. It gives judgment better information.

Lessons from AstraZeneca Spain: structured cross-functional alignment

The AstraZeneca Spain case is useful because it points to a structural response rather than another appeal for better cooperation. The documented model involved four cross-functional teams:

1. Early Asset Strategy Team

2. Launch Readiness Team

3. Core Value Team

4. Brand Team

The important lesson is not to attach unverified timings, responsibilities, or handoff rules to those names. The value of the model lies in recognizing that different stages and strategic questions require different forms of cross-functional alignment.

An early asset discussion is not the same as an in-market brand discussion. Launch preparation is not the same as the ongoing work of demonstrating value. A team that is designed to bring functions together around one strategic question should not automatically be expected to govern every other question in the asset’s lifecycle.

That sounds obvious, but many organizations create one broad cross-functional committee and then ask it to handle everything: evidence, launch planning, stakeholder engagement, field execution, lifecycle decisions, and conflict resolution. The result is a meeting that is too large for operational decisions and too general for strategic ones.

The four-team structure offers a different way to think about the problem. It creates distinct forums around distinct alignment needs while keeping Medical Affairs and Commercial involved in the same wider asset strategy.

What the case demonstrates

The case demonstrates several principles that can be applied beyond one country organization or company.

First, cross-functional governance should follow the asset’s strategic questions.

Teams should exist because a recurring decision or coordination problem needs a home, not because the organization wants to display collaboration.

Second, the presence of Medical and Commercial in the same structure does not erase their different responsibilities.

A functional boundary can remain intact while the teams collaborate around shared decisions. This is preferable to creating ambiguous hybrid roles that blur accountability without resolving the underlying conflict.

Third, naming the forums matters.

A team with a clear strategic purpose is easier to convene, staff, and evaluate than a generic committee whose remit expands whenever a new problem appears.

Fourth, alignment needs a place in the operating model.

If collaboration depends entirely on informal relationships between individuals, it will weaken when people change roles, priorities shift, or an asset enters a more pressured phase.

The case should therefore be read as an example of structured coordination, not as proof of a single universal template. Other organizations may need different teams or different governance layers. The transferable principle is to make the points of collaboration visible and intentional.

The boundaries between Medical Affairs and Commercial can remain firm without becoming walls. The work is to build the doors, define when they open, and make sure someone is responsible for using them.

Redefining internal governance to foster scientific and commercial synergy

What should a Medical Affairs leader do when the organization recognizes the problem but continues to behave as though better intentions will solve it?

Start by treating the silo as an architecture problem rather than a personality problem. Culture matters, but culture is shaped by incentives, reporting lines, planning cycles, data access, and decision rights. A workshop can improve relationships. It cannot, on its own, resolve a planning-horizon mismatch or clarify who owns a cross-functional decision.

The next step is to examine the actual engagement pattern rather than relying on perceptions of collaboration. Select a representative group of strategically important stakeholders and reconcile the relevant outreach across field medical, Commercial, medical information, and other participating functions. The purpose is not to audit individuals. It is to reveal whether the organization’s external behavior matches its stated intent.

The review should look for:

• repeated or poorly sequenced contacts;
• unclear ownership of stakeholder relationships;
• inconsistent descriptions of the same evidence;
• activities that are recorded in one function but invisible to another;
• decisions that have no clear escalation route;
• insights that enter a function but do not travel across the organization.

This type of review often produces a more useful picture than an employee survey. People may sincerely believe collaboration has improved because communication is more frequent. The field may still be experiencing the consequences of fragmentation.

Build governance around decisions, not attendance

A cross-functional forum should have a defined reason to exist. Before creating or expanding one, leadership should be able to answer:

• What decision belongs here?
• Which functions must be represented?
• What information is required before the decision can be made?
• Who has final authority?
• How will the decision be communicated and implemented?
• When will the decision be revisited?

These questions prevent the familiar failure mode in which every function is invited but no function is accountable. Attendance becomes a substitute for governance.

The same principle applies to escalation. Not every disagreement deserves senior intervention, but every recurring disagreement should have a route through which it can be resolved. If Medical Affairs and Commercial repeatedly disagree about an external engagement, evidence interpretation, or launch dependency, the organization should not rely on the individuals involved to negotiate from scratch each time.

A useful escalation model distinguishes between:

• disagreements about scientific interpretation;
• disagreements about permissible communication;
• disagreements about prioritization and resource allocation;
• disagreements about timing;
• disagreements about stakeholder ownership.

Different disputes may require different decision-makers. Treating them all as interpersonal conflict is inefficient and unfair to the people asked to resolve them.

Make the medical plan strategically legible

Medical Affairs also has a responsibility to explain its work in terms that other functions can use. Scientific rigor should not require strategic opacity.

A medical plan should make clear:

• which questions it is designed to answer;
• why those questions matter to patients, HCPs, payers, investigators, or the broader healthcare system;
• what evidence already exists;
• what uncertainty remains;
• which activities are essential and which are contingent;
• how progress will be assessed without reducing scientific work to simplistic volume metrics.

This does not mean converting Medical Affairs into a commercial function. It means making the consequences of medical decisions visible to colleagues who are responsible for other parts of the asset strategy.

Commercial teams, in turn, need to engage with the medical plan before they require its outputs. Evidence cannot be treated as a last-minute input to a campaign, a launch meeting, or a market-access narrative. Early involvement allows the organization to identify where the evidence is strong, where it is still developing, and where claims or expectations need to be moderated.

Assign coordination accountability carefully

Many organizations recognize the need for coordination but assign it to everyone, which usually means that nobody owns it. A cross-functional lead, program owner, or governance office can help, but the role must be defined carefully.

The coordinator should not become a substitute for functional leadership. Nor should the role be a ceremonial chairmanship with no authority to surface difficult issues. Its value lies in maintaining the connective tissue between plans, forums, decisions, and stakeholder activity.

At minimum, that responsibility should include:

• keeping the relevant planning processes connected;
• identifying conflicts before they reach the field;
• ensuring that decisions are documented and communicated;
• tracking unresolved dependencies;
• escalating issues when the existing governance route is insufficient.

The exact title matters less than the clarity of the mandate. Coordination becomes real when someone is expected to notice misalignment early and has enough access to bring it into the right forum.

From visible collaboration to strategic integration

The pharmaceutical industry may be more collaborative on paper than it was in the past. More functions are represented in planning meetings. More organizations use shared language around patient value, evidence, and stakeholder engagement. More leaders acknowledge that Medical Affairs and Commercial cannot operate as unrelated businesses.

That progress is meaningful, but it is not the same as strategic integration.

The real test is whether the organization can turn internal alignment into a coherent external experience. Can an HCP understand why the company is engaging, what evidence is relevant, and how different interactions fit together? Can field teams access the context they need without compromising functional independence? Can leaders identify a conflict early enough to resolve it before it becomes a stakeholder problem, a missed opportunity, or a compliance concern?

Medical Affairs cross-functional collaboration failures are rarely caused by a complete absence of goodwill. More often, they are produced by systems that reward local optimization. Commercial protects the quarter. Medical Affairs protects scientific quality. Field teams protect their relationships. Brand teams protect execution. Each may be acting rationally within its own structure while the organization performs poorly as a whole.

The answer is not to eliminate those responsibilities. It is to connect them deliberately through shared planning, clear decision rights, coordinated stakeholder visibility, and governance that follows the asset’s actual strategic questions.

The strongest organizations do not make Medical Affairs and Commercial identical. They make the relationship between them legible. They know where collaboration is required, where independence is essential, and who is accountable when the two come into tension.

The question is no longer whether Medical Affairs and Commercial should collaborate. It is who in the organization is accountable when they do not.