We describe a patient with bronchiolitis obliterans organizing pneumonia (BOOP) requiring respiratory support and treated with corticosteroids and cytoxan for presumed Wegener's granulomatosis (WG). The diagnosis of WG was based on clinical presentation and strongly positive stains for anti-neutrophilic cytoplasmic antibodies (cANCA). The results of an open-lung biopsy were consistent with BOOP. Although BOOP has previously been described as one of the pulmonary manifestations of WG, other more specific histologic features of WG such as capillaritis or necrotizing vasculitis were lacking. Because influenza A virus was cultured from the patient's lung tissue, final assessment of the illness focused on this as the etiologic agent triggering the pulmonary syndrome. The presence of ANCA was considered to be nonspecific. The patient's condition improved with appropriate therapy for BOOP.