Wegener granulomatosis (WG) belongs to a heterogeneous group of systemic anti-neutrophil cytoplasmatic antibody (ANCA) associated vasculitides (AASV). WG is characterized by necrotizing granulomatous inflammation of the upper and lower respiratory tract, glomerulonephritis and vasculitis. As a multifactorial model disease, WG is hallmarked by the presence of specific ANCA-subtypes directed against a defined antigen. WG is more predominant among Caucasians and the genetic predisposition appears quite complex. Here, we provide a brief overview concerning genetic factors in the pathogenesis of WG and discuss intricacies of molecular genetic approaches.