Zickler played in 24 league games – scoring three goals – in 2000–01 as Bayern won the league. In the campaign's UEFA Champions League final, against Valencia CF, he entered the game as a substitute and successfully converted his penalty kick in the shootout, which ended in win. During his time in the top flight, he broke the record as the highest goal-scoring substitute of all-time, scoring 18 times in 102 appearances off the bench; however, his career was often hampered by injuries and medical conditions: in 2002, he had surgery to remove a tumor from his right shin bone which caused him to miss out on participation in the 2002 FIFA World Cup. One year later, he was again hospitalized with a break in his previously operated leg, followed by another shin break only a few days before the start of 2003–04.