The qualifying groups for the 2006 UEFA European Under-21 Championship, where possible, matched the 7- and 6-team World Cup 2006 qualifying groups of the senior European teams. The exceptions were where Andorra, Faroe Islands, Liechtenstein, and Northern Ireland were involved; none of whom entered an under-21 team. Germany, whose seniors did not need to qualify for the World Cup (as they will be hosts) were added to one of the 5-team groups created by the absence of the aforementioned nations.

Europe's 48 national under-21 teams entering were divided into eight groups (six groups of 6 + one group of 5 + one group of 7). The eight group winners played off against the eight group runners-up on a two-legged home-and-away basis to decide the eight qualifying teams.