Organ transplantation is currently the standard therapy for patients with end-stage organ dysfunction. The immunosuppression caused by this therapy increases the rate of infection, particularly in the lungs. Early diagnosis is extremely important and fibre-optic bronchoscopy is a helpful tool in reaching diagnosis. Knowing the timing of various pathogens following transplantation, and the radiological picture as well as the prophylactic regimen, is helpful when specific pathogens are suspected. Bronchoscopy with bronchoalveolar lavage and transbronchial biopsies are particularly helpful in diagnosis of bacterial cytomegalovirus (CMV) and pneumocytosis carinii pneumocytosis, and is considered a safe procedure. Open lung biopsy is reserved for those who have negative bronchoscopy with a reasonable prognosis.