In 2001, he joined Borussia Dortmund, where he won the Bundesliga title in his first season and scored 73 goals in 167 official games over five campaigns.

Koller is the all-time top scorer for the Czech Republic national team, with 55 goals in 91 appearances in a decade-long career starting in 1999.

He quickly built up a successful partnership with Canadian striker Tomasz Radzinski, excelling in his debut season and earning him the Belgian Golden Shoe in 2000.

Besides the Bundesliga title his biggest success whilst at Dortmund was helping them to the 2002 UEFA Cup Final, where his goal could not prevent them losing 3–2 to Feyenoord.

[10] Unfortunately for Koller, who wasn't the only Czech in the team as he was partnered with Tomáš Galásek and Jaromír Blazek, the Nürnberg-based club had performed poorly throughout the season and were relegated to 2.

[3] Koller made his debut for the Czech Republic in a friendly away to Belgium at the King Baudouin Stadium in Brussels on 9 February 1999, and netted the only goal of the game in the 73rd minute.

[14] Koller became the all-time top scorer for the Czech Republic on 8 June 2005 following a match against Macedonia, in which he scored four goals in just 11 minutes of a 6–1 win, taking his international total to 39.