Kirsten was one of the first East German footballers to enter the Bundesliga after the German reunification. In the German Bundesliga he played 350 matches for Bayer 04 Leverkusen and scored 182 goals (ranked #7 in the all-time top scorer list). He established himself as one of the most dangerous strikers in the Bundesliga, but Bayer Leverkusen regularly ended as runner-up to either Bayern Munich or Borussia Dortmund. He stayed there until his retirement in 2003. He also played in the 2002 UEFA Champions League Final. In the 1999–2000 season, Kirsten won the EFFIFU award for being the most efficient striker in the league.