In the end he decided to accept an offer from German Bundesliga Team Bayer 04 Leverkusen, who were part of the Champions League and signed a 5 Year deal at the German Club.
At Bayer 04 Leverkusen, for the first time in his career, Emanuel Pogatetz played alongside world-class players like Michael Ballack, Lucio, Ze Roberto, Ulf Kirsten, Jens Nowotny and many more. Under Head-Coach Klaus Toppmoeller he featured in his first game for Bayer 04 Leverkusen when playing in the German League Cup against Hertha BSC Berlin.
Emanuel Pogatetz was part of a very successful team which was able to reach the Champions League Finale and also came very close to win the German Double.
He was also able to earn himself a spot in the Austrian National Team during this time.
Under Head-Coach Hans Krankl he made his debut in the game against Germany, when he came on in the 83. Minute, of all things to be played at Leverkusen. Although the game was lost 6:2, it was a very special and proud moment in the career of Emanuel Pogatetz.