 Articles that Whitaker co-wrote won the 1998 George Polk Award for Medical Writing and the 1998 National Association of Science Writers’ Science in Society Journalism Award for best magazine article.A 1998 "Boston Globe" article series he co-wrote on psychiatric research was a finalist for the 1999 Pulitzer Prize for Public Service.In April 2011, IRE announced that "Anatomy of an Epidemic" had won its award as the best investigative journalism book of 2010 stating, "this book provides an in-depth exploration of medical studies and science and 
intersperses compelling anecdotal examples.