Bronchoscopy with bronchoalveolar lavage (BAL) is a frequently performed, minimally invasive endoscopic examination in patients with unclear infiltrates or pulmonary infections. It can be performed safely in patients with compromised immune systems of different etiologies. This article summarizes the experience with and efficacy of BAL in different disease states in this clinical circumstance. Because human immunodeficiency virus (HIV)-related diseases and acquired immune deficiency syndrome (AIDS) patients show different characteristics when compared with patients with other reasons for immunosuppression, they are discussed separately. Clinical algorithms are presented.