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What Life Sciences Companies Get Wrong When Building Cross-Border R&D Structures

These structures, if not set up and managed correctly from day one, can create significant accounting, tax and compliance headaches down the road.

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Cross-border structures in life sciences are no longer the exception; they are the rule. Whether it’s an Israeli biotech starting up a U.S. subsidiary to tap into the talent pipeline flowing out of MIT or Stanford, a Chinese-founded company organizing its IP ownership stateside to attract U.S. venture capital, or a European pharma company establishing a U.S. entity to run clinical trials closer to the FDA, inbound structures have become table stakes in the industry.

What remains underappreciated is how much these structures, if not set up and managed correctly from day one, can create significant accounting, tax and compliance headaches down the road. The companies that navigate this smoothly aren’t necessarily the ones with the biggest budgets. They are those that treat financial and tax infrastructure as a strategic priority from the moment they incorporate in the U.S.

Foreign life sciences companies establish U.S. operations for many reasons including to gain access to a deep, specialized talent pool, proximity to leading academic medical centers and major research hospitals, stronger IP protections and U.S. investors. As the funding environment for life sciences has grown more selective, there is an increasing preference among institutional investors for U.S.-based entities that own the IP and conduct research and development (R&D) domestically. The perceived risk of investing in a purely foreign entity, particularly amid ongoing geopolitical and currency uncertainty, has made U.S. subsidiary formation even more attractive as a fundraising strategy. Further, investors often prefer U.S.-based entities that hold clear title to IP because it simplifies enforcement, due diligence and exit planning.

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The cost of living and operating differential is significant, and foreign founders often experience sticker shock when they see how payroll and lab space cost in the U.S. compared to their home country. But the tradeoff in terms of investor access and market credibility is often worth the expense.

One of the first questions companies need to think through is where the R&D activity “lives,” both legally and financially. This is often decided by legal counsel and based on IP ownership strategy.

In the most common inbound structure, a foreign parent company funds a U.S. subsidiary, which hires the research team, incurs the R&D expenses, and then invoices the parent company to be reimbursed for those costs plus a markup. This is called a cost-plus arrangement, and while this approach is relatively straightforward in concept, two elements consistently create risk and confusion.

1. Documentation 

Transfer pricing rules require that intercompany transactions occur at “arms-length,” meaning the pricing and terms must mirror what unrelated parties would negotiate in similar circumstances. Tax authorities scrutinize these arrangements closely. A cost-plus arrangement between related parties needs to be supported by a formal intercompany agreement that defines the markup percentage, the billing cadence, and the scope of reimbursable costs. What is less commonly understood is that this agreement cannot simply be signed, executed and forgotten. It must reflect what the parties are doing in practice, and it should include triggers for revisiting the arrangement as the company’s business model evolves. For example, a company that starts out doing pure R&D as a cost center may eventually transition to US product distribution, causing a shift away from cost-plus entirely. Without proper documentation of this transition, companies may face risks during an IRS examination or M&A due diligence.

2. Intercompany cash flows:

Another concern is that if the parent company is slow to pay the cost-plus invoices to the U.S. subsidiary, the subsidiary can find itself in a cash flow challenge, even scrambling to make payroll. Building clarity around the timing and mechanics of intercompany transfers and maintaining accurate records of all intercompany balances is an operational necessity that some companies underestimate until a crisis hits.

One of the advantages of conducting R&D in the United States is access to the Federal Research Tax Credit. The credit allows companies to offset current or future income taxes. An additional benefit applies to pre-revenue early-stage companies in their first five years of existence, who may elect to apply up to $500,000 per year to offset future payroll taxes. For a company burning through cash while waiting on clinical trial results, that represents a meaningful and fast way to generate cash flow.

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But the R&D tax credits are only as useful as the underlying documentation that substantiate true R&D costs. The credit includes a 20-year carryforward period, and the IRS has the right to examine the underlying records in the year the credits are used, not just the year they were generated. That means an unprofitable company that (a) earns a credit in Year 3 and (b) doesn’t generate taxable income until Year 15, must have documentation from Year 3 that can survive scrutiny a decade and a half later. This is the kind of nuance that can have a tremendous impact when a company finally reaches profitability and tries to benefit from those accumulated credits.

Beyond federal incentives, state-level programs can be significant. Massachusetts, for example, has a Life Sciences Center that offers additional tax credits to qualifying companies that meet specific hiring milestones. Choosing where to locate is never purely a tax decision, as there are several other factors, but understanding the tax environment of different states is worth building into the analysis early on.

The risk of exposure to this issue is not limited to under-resourced start-ups. Even experienced operators can be caught off guard. A standard document retention policy of five to seven years can inadvertently create gaps in records that were generated 15 years ago and are only examined when the need arises. 

Cap table management is another area where issues surface. The cap table is a verified, detailed record of ownership percentages, share types and investor identities. An “ownership change” exceeding 50% over a three-year period under IRS rules can potentially trigger usage limitations on pre-change losses and credits or affect how future losses and credits are utilized. Companies expecting significant financial events (fundraising round, M&A, IPO, etc.) need to proactively track any developments that may influence the carryovers. In addition, the structure and documentation of stock-based compensation used in lieu of salaries to attract talent need to be airtight as well.’

The practical takeaway is that the best time to build clean financial and tax infrastructure is before you need it. Cross-border R&D structures work. They are efficient, strategically sound, and they reflect the global nature of life sciences innovation. But like any complex structure, they require ongoing attention to the details that do not make the headlines. That attention pays off when it matters most, for instance, when they are headed into a funding round. Companies heading into a Series A or B or M&A due diligence are under closer scrutiny than they were a few years ago. Investors and acquirers want to see accurate records and the ability to produce them quickly. Discovering gaps in transfer pricing documentation or R&D credit support at that stage, is a significantly more expensive problem to fix than building the systems correctly from the start. It’s important to know that and create infrastructure from the creation of the U.S. subsidiary to achieve success.

Photo: sesame, Getty Images

Destiny J. Flood, CPA, is a Partner at AAFCPAs and leads the firm’s Commercial Division within its Outsourced Accounting & Fractional CFO practice. She oversees a national team of fractional CFOs, controllers, and accountants delivering financial reporting and advisory services to privately held companies across industries. Destiny brings more than 15 years of experience in public accounting, with a background in audit and technical accounting that informs her work with business owners, leadership teams, and investors.

Her areas of focus include financial reporting, internal controls, complex transactions, and operational process improvement. She and her team provide full outsourced finance functions and advise on mergers and acquisitions, revenue recognition, and inventory accounting, helping organizations strengthen financial oversight and reduce risk. Destiny holds a Bachelor of Science in Professional Accounting, magna cum laude, from Eastern Washington University. She is a statewide board member for CalCPA and is an AICPA council member.

Richard L. Weiner specializes in tax planning and consulting for privately and publicly held domestic and multinational businesses. He advises clients in the life sciences, software, publishing, manufacturing, and professional services industries, helping them streamline operations, maximize tax savings, and ensure compliance. Rich is a leader in AAFCPAs’ Business Transaction Advisory practice, supporting clients through M&A processes, restructurings, and other similar transactions, from advance planning to deal origination to closing, and guides business owners and executives through ownership transitions with long-term tax strategies.

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