Pozzato turned professional in 2000 with the Mapei cycling team, part of the famous classe di ’81 a group of emerging young riders born in 1981 who were part of the Mapei TT3 development team.
After Mapei ended its sponsorship in 2002 Pozzato joined Giancarlo Ferretti’s Fassa Bortolo cycling team. Despite his win of Tirreno-Adriatico in 2003 and a stage win in the 2004 Tour de France, personality clashes with Ferretti meant that Pozzato suffered poor years with Fassa Bortolo in 2002-2004. During this period he was injured for some time and had to work for star sprinter Alessandro Petacchi at other times.
During the 2004 season he was chosen to be part of the winning Italian 2004 Olympics team in support of team leader Paolo Bettini. He re-established contact with several managers and directeurs sportif of Quick Step-Innergetic. The Quick Step-Innergetic team expressed interest and Pozzato was able to obtain a release for the 2005 ProTour season, joining several former Mapei riders already on the team, such as Paolo Bettini and Davide Bramati.
The 2005 ProTour season went better for Pozzato, with a win in the HEW Cyclassics in front of teammate Luca Paolini.
The 2006 season saw him win the first major classic of the year Milan-Sanremo after a superb ride which saw him first work for team leader Tom Boonen, but then was forced to launch his own winning attack in the finale.
For the 2007 season, Pippo joined the Liquigas squad, and began his season in style, winning the Tour du Haut Var the Omloop Het Volk and Stage 5 of the Tour de France.