Ivan Ljubičić won the title, defeating Stefan Koubek 6–3, 6–4 in the final.
Seeds
Ivan Ljubičić (champion) David Ferrer (first round) Richard Gasquet (second round) Radek Štěpánek (second round) Mario Ančić (second round) Jarkko Nieminen (second round) Igor Andreev (first round) Feliciano López (second round)
Draw
Finals
Top half
Bottom half
External links 2006 PBZ Zagreb Indoors draw 2006 PBZ Zagreb Indoors qualifying draw