The records of 9 adult male patients with the acquired immune deficiency syndrome (AIDS) and biopsy-proved Pneumocystis carinii pneumonia were reviewed to determine the correlation between serial pulmonary function tests and the presence or absence of Pneumocystis organisms in subsequent bronchoscopy specimens. At diagnosis, total lung capacity (TLC) or vital capacity (VC) was abnormally low in 4 patients (44%) and diffusing capacity (DLCO) was abnormally low in 8 patients (89%). The ratio of forced expiratory volume in one second (FEV1) to forced vital capacity (FVC) was elevated in all patients. After 21 to 47 days of specific therapy for Pneumocystis pneumonia, changes in DLCO, TLC, VC, and FEV1/FVC did not correlate with the presence or absence of Pneumocystis organisms in bronchoscopy specimens from 7 patients. However, changes in DLCO 105 to 258 days after diagnosis seemed to correlate with the late response to treatment in 6 patients. These results suggest that decisions to terminate specific therapy for Pneumocystis pneumonia in patients with AIDS should not be based on short-term changes in pulmonary function.