On January 30, 2009, it was revealed that Nitkowski was interviewed by the FBI as part of its investigation into the perjury case against Roger Clemens. Nitkowski worked out sporadically in the off-seasons from 2001–2006, while also being trained by Brian McNamee, Clemens' principal accuser. Nitkowski, in a statement to the Associated Press (an organization he also occasionally contributes to as a writer) said, "I have never seen Roger or Andy take any illegal performance-enhancing drugs. I have never talked to either of them about PEDs, nor do I have any firsthand knowledge of them taking any PEDs."