In his first season for Hannover 96, 1998-99, he made four matches in the team which played in the 2nd German league (2. Bundesliga). In the following season, Cherundolo was in the team most of the time, but he had a bad knee injury. He came back during the 2000-01 season and made 18 matches. In the following season, he made 33 of 34 matches and has been a start member of the team most of the time until 2008. 