Pulmonary vasculitis is a potentially lethal autoimmune disease characterized by granulomatous inflammation of respiratory tract, necrotizing vasculitis affecting small-to medium-size vessels and antineutrophil cytoplasmic antibodies elevation. Typical therapy involves high-dose glucocorticosteroids combined with cyclophosphamide in a dose 1-2 mg/kg/per day. A high relapse rate in pulmonary vasculitis means prolonged courses of cyclophosphamide in some patients. Carcinogenic effects of cyclophosphamide, especially its toxic metabolite acrolein that is excreted into the urine, are responsible for the development of acute myeloid leukemia (AML) and bladder cancer. These and other malignancies are cyclophosphamide dose-depended. The aim of the present study was to assess the incidence of cancer in patients with pulmonary vasculitis in comparison with the incidence of cancer in the general population. Analyses were done according to the cumulative dose of cyclophosphamide, subdivided into low (≤35 g) and high (>35 g). During the observation period 15 cancers occurred. A significantly increased standardized incidence ratio (SIR) was observed for non-melanoma skin cancers (SIR 5.2; 95 % Cl 2.3-8.7), AML (SIR 4.3; 95 % Cl 2.1-11.2), and bladder cancer (SIR 3.4; 95 % Cl 1.6-5.2). Induction remission treatment and relapse treatment with cyclophosphamide involves a substantial risk of late appearing malignances in patients with pulmonary vasculitis. Monitoring and prophylactic management in pulmonary vasculitis after cessation of cyclophosphamide therapy is crucial.