In the middle of the 1999–2000 season, Guidolin joined Serie A side Bologna, a former club as a player. Despite finishing ninth in the previous season, Bologna had qualified for the 1999–2000 UEFA Cup after winning a tie-breaker against Internazionale. Guidolin took them to the third round of the UEFA Cup, where they were eliminated by Galatasaray. In the Serie A season, they finished in 11th place. The following league campaign ended with another ninth-place finish, followed by another small improvement to seventh place and entry into in a summer tournament, the 2002 UEFA Intertoto Cup, where they were defeated in the three-game final stage by Fulham.