Viruses and bacteria in bronchoalveolar lavage fluids, protected specimen brush samples, and bronchial biopsies from 14 patients with primary hypogammaglobulinemia (11 patients with common variable immunodeficiency [CVID] and three patients with X-linked agammaglobulinemia [XLA]) were analyzed. At the time of the study, the patients had no signs of acute respiratory infections, and no antibiotics were administered. In addition to routine bacterial and viral cultures, polymerase chain reaction tests were used for the detection of adenovirus, cytomegalovirus (CMV), herpes simplex virus 1, enterovirus, rhinovirus, Borrelia burgdorferi, Chlamydia pneumoniae, Legionella spp., Mycoplasma pneumoniae, Pneumocystis carinii, and Ureaplasma urealyticum. Viruses (four adenoviruses, one CMV, and one rhinovirus) were detected in four of the 11 (36%) CVID patients. No viruses were found in the three patients with XLA or in 13 control patients. Bacteria from the lower respiratory tract were detected in nine of the 14 (64%) patients with hypogammaglobulinemia and three of the 13 (23%) control patients. Haemophilus influenzae was the most prevalent bacterium (43%) in the hypogammaglobulinemia patients. The study shows that patients with CVID harbor viral and bacterial infections in the lower respiratory tract, which may predispose to the development of changes in the respiratory tract.