Her claim about the funding of NIH is not accurate, no matter how you slice the numbers.
Regardless of which years you choose to compare, or whether the numbers are adjusted for inflation, funding went up.
In non-inflation-adjusted dollars, funding increased. Bush requested $28.9 billion dollars in net budget authority for fiscal 2008 (the year that began Oct. 1, 2007), and the agency received an estimated $28.6 billion in fiscal 2007. Either of these numbers is greater than when Bush came into office -- $20.6 billion in fiscal 2001, the last year for which Clinton presided over the congressional budgeting process, or $17.8 billion in fiscal 2000, the last full fiscal year Clinton was in office.
The numbers tell the same tale for net outlays, with an estimated $28.1 billion in fiscal 2007 compared with $17.3 billion and $15.4 billion for fiscal 2001 and 2000, respectively.
The increases aren't as large when the numbers are adjusted for inflation. But they still went up.
In response to an inquiry from PolitiFact, the Clinton campaign provided two newspaper stories that said the NIH budget had been flat since 2003. We acknowledge that is accurate, but we still find funding has gone up during Bush's presidency. We find her statement to be False.