Although Bišćan was originally signed as a central midfielder, Gérard Houllier felt he was more useful as centre back and often played Bišćan out of his natural position, sometimes even as a winger or full back. Bišćan fell out of favour after his first year at Liverpool, making only 23 appearances in the next two seasons. During this time, he made few starts and spent a total of 37 matches on the bench without being used as a substitute. A major injury crisis of the team in 2003–04 season gave Bišćan a comeback chance, and by the start of the new Premier League season, he had returned into the starting 11, featuring regularly as a centre-back in the absences of Stéphane Henchoz and Jamie Carragher. By the end of the season, Bišćan featured in 39 matches, 30 of which he played the entire 90 minutes. He was sent-off in 36th minute of Liverpool's UEFA Cup second leg match against Marseille, which turned things around for Liverpool as they were eliminated from the competition, after which he struggled to regain his place.