Federal research funding remains protected against proposed cuts, but policy and personnel instability threaten university research operations. The National Institutes of Health avoided direct funding reductions, yet more than half of its 27 institutes and centers lack permanent leaders, leaving them run by acting directors. Separately, the Trump administration’s push to cap indirect research costs has been checked by Congress and courts, halting implementation of new reimbursement rules. Universities face uncertainty over overhead rates, grant negotiations and continuity at NIH, complicating strategic research planning and faculty hiring.