As a result of an injury, he missed most of the 2002–03 season. In the fall of 2003, he played in crucial UEFA Euro 2004 qualifying matches for Poland. Unfortunately, Poland was unable to qualify and 1. FC Nürnberg was unable to stay in the Bundesliga. As a result of his excellent play, he was transferred to a top Bundesliga club, Bayer Leverkusen. In the 2004–05 season, he was one of the best players for the club, and the trio of Krzynowek, Andriy Voronin, and Dimitar Berbatov drew the attention of many top European clubs. Bayer Leverkusen also played very well in the Champions League, where it eliminated such clubs as Real Madrid and A.S. Roma. Krzynowek scored three goals, one of which was scored versus Real Madrid, which was named one of the most beautiful goals in that year's tournament.