Koubek tested positive for glucocorticosteroids at the 2004 French Open after receiving an injection for an injured wrist; he was subsequently suspended for three months.
Koubek reached the fourth round in his French Open debut, losing to Àlex Corretja; to date, this is his best performance at this event.
Koubek made the final of Bournemouth, losing to Adrian Voinea, and helped his country Austria back into the World Group of Davis Cup by defeating Sweden 3–2 in a promotion tie.
At the 2000 French Open, in his match against Attila Sávolt (the score being 2-1 sets and 5-2 games in favour of his opponent), after having already received three warnings for various transgressions, Koubek was disqualified due to throwing his racket and accidentally hitting a ball boy.
Koubek won the tournament without dropping a set, defeating Jan-Michael Gambill in the final, and briefly holding the top spot in the ATP Champions Race.
Koubek's form remained inconsistent, again losing seven consecutive first-round matches after his victory in Doha, before making the semi-finals in Munich, where he lost to Roger Federer.
In Davis Cup, Koubek defeated the Belgian brothers Christophe and Olivier Rochus to help return Austria to the World Group.
In Thomas Muster's debut as Davis Cup captain, Koubek was instrumental in preserving Austria's status in the World Group, winning both singles matches over Tim Henman and Greg Rusedski.
Koubek tested positive for glucocorticosteroids at the 2004 French Open after receiving an injection for an injured wrist; he was subsequently suspended for three months.
His best results on the tour were a third round in Kitzbühel, losing to Nicolás Massú, and a semifinal in the Helsinki Challenger, where he lost to Björn Rehnquist.
Koubek was disqualified in Metz against Sébastien Grosjean while leading 4–2 in the final set after using abusive language to the tournament supervisor Thomas Karlberg while disputing a call.
In March Koubek suffered back problems and will have surgery to alleviate bulging discs, which is a potentially career threatening injury.