Von Eschenbach was president-elect of the American Cancer Society when he was selected by President George W. Bush to head the NCI in December 2001.

However, under von Eschenbach's leadership the FDA has been criticized for being too risk averse when considering life saving treatments for desperate, dying patients.

For example, in 2007 the FDA failed to approve Provenge for the treatment of late stage prostate cancer against the recommendation of an independent advisory committee.

"[5] In 2006, Time named him as one of the Time 100 "People Who Shape Our World", writing that as head of the FDA, which "wields enormous influence on American lives", von Eschenbach "could make a signal contribution to the public's health" by focusing on issues of diet and obesity in addition to drugs and disease.

On August 1, 2006, Senators Clinton and Cantwell announced they would block his nomination to be the permanent FDA commissioner because of his department's failure to act on the application by Barr Pharmaceuticals to sell Plan B over-the-counter.