At the start of 2001–02 season, Baggio scored eight goals in the first nine matches, leading him to the top of the Serie A goalscoring table. In his eighth league appearance of the season, against Piacenza, Baggio scored a goal but later suffered an injury. A week later, against Venezia, he scored from a penalty, but he endured a more serious injury following a hard challenge which caused him to tear the ACL of his left knee, keeping him out of action for four months. He suffered a second serious injury that season, tearing the meniscus in his left knee, after returning to the team, and coming off the bench, in the Coppa Italia semi-final against Parma on 31 January 2002. He was operated on 4 February 2002 and he returned for three matches before the end of the season, making a recovery in 76 days. On 21 April 2002, in the first game after his comeback, Baggio came on as a substitute to score two goals against Fiorentina, helping Brescia win the match. He scored again against Bologna, saving Brescia from relegation on the final matchday, and bringing his seasonal tally to 11 goals in 12 Serie A matches. Despite Baggio's performances and public demand, Italy national team head coach Giovanni Trapattoni did not deem him fully fit, prompting the coach to leave Baggio out of the final squad for the 2002 World Cup. Trapattoni also expressed concern about bringing Baggio to the World Cup due to the presence of Francesco Totti and Alessandro Del Piero in his role, believing that this could create a rivalry between the players. After missing out on the tournament, Baggio reversed his initial decision to retire after the World Cup, expressing his intention to surpass the 200 Serie A goal mark.