After finishing third overall in the 2009 Giro, he won the polka dot jersey in Paris as the best climber of the 2009 Tour de France (which has been cancelled), as well as named the Most Combative (Aggressive) Rider on Stages 9 and 17.

On 3 May 2010, Pellizotti's name was released by La Gazzetta dello Sport as being one of several riders under investigation by the Union Cycliste Internationale (UCI) for "irregular blood values".

Pellizotti was reported to have had "suspicious values" on the eve of the 2009 Tour de France and request has been made by the UCI for investigation.

[3] He was due to be one of Liquigas–Doimo' team leaders at the 2010 Giro d'Italia, but was immediately pulled from the squad and replaced with Vincenzo Nibali.

[4] Shortly after the end of the season, the suspension was lifted on the grounds of lack of evidence, and Pellizotti declared a wish to seek financial redress from the UCI.