The New H-1B Rules and the American Research Apparatus

USCIS has announced two sweeping changes to the H-1B visa system that will reshape how the United States recruits global talent: a new $100,000 government filing fee for most new H-1B petitions and a shift from a random lottery to a wage-weighted selection system that favors higher-paid workers. Together, these rules mark a major reorientation of the program—from broad talent access toward a pay-to-play model that carries serious consequences for universities and nonprofit research institutions, which remain the core of the American research apparatus.

Under the new selection system, H-1B registrations will be “weighted” based on wage level. Employers offering higher salaries will receive more chances in the lottery, materially improving their odds of selection. USCIS finalized this approach in December 2025 despite extensive public comments warning that it would disadvantage early-career professionals, nonprofits, and academic employers.

At the same time, a new $100,000 filing fee—designed as a deterrent to foreign hiring—has been layered onto most new H-1B petitions, which could have a chilling effect on international recruitment. Now, it bears mentioning that American universities and nonprofit research organizations technically remain “cap-exempt,” meaning they do not participate in the H-1B lottery itself. But this formal exemption masks deeper structural risks.

First, the six-figure fee sharply increases the cost of recruiting international researchers, post-doctoral fellows, and faculty from abroad—a key component of the workforce on which many nonprofit research institutions depend. Unlike private-sector employers, universities and nonprofit labs operate on fixed grant budgets and salary bands. A single H-1B hire could now consume a nontrivial portion of a research grant, forcing institutions to reconsider whether to recruit internationally at all.

Second, wage-weighting in the broader H-1B market will push private-sector salaries higher, widening an already significant compensation gap. As industry employers respond to the new incentives, universities and nonprofits will find it even harder to compete for top STEM graduates trained in U.S. institutions. The likely result is reduced international student retention, weakened early-career research pipelines, and increased “brain drain” toward better-resourced private firms.

Public comments on the rulemaking process specifically warned that these changes would undermine international student pathways and disproportionately harm nonprofit and academic employers. Those warnings aren’t abstract. They reflect how modern research actually functions: through globally mobile talent, grant-funded teams, and long-term investment in early-career scientists. In effect, the H-1B program is being transformed into a market instrument that privileges capital over mission. For higher education and nonprofit research institutions, this shift quietly but profoundly alters the economics of discovery—and with it, the future of the innovation sector in the United States.

CJR