The sensitivity of Pneumocystis carinii detection using silver stain (Grocott method) was compared to that using the avidin-biotin-complex immunoperoxidase (IP) staining method with anti-P. carinii monoclonal antibody. Silver stain detected only cyst wall, whereas IP stained both cyst wall and trophozoites. Serial sections of formalin-fixed, paraffin-embedded autopsy lung specimens from 41 acquired immune deficiency syndrome patients in three disease categories were stained: I--premortem or autopsy diagnosis of P. carinii pneumonia (13 cases); II--history of treated P. carinii pneumonia but no P. carinii detected in autopsy tissue specimens (15 cases); and III--no clinical or autopsy evidence of P. carinii pneumonia (13 cases). Smears from 7 bronchoalveolar lavages (3 positive) and 11 induced sputa (1 positive) also were stained. All cases of P. carinii in category I were detected with equal sensitivity. P. carinii undetected by silver stain in category II and III cases and in bronchoalveolar lavages and induced sputa were not revealed by IP. Detection of trophozoites by IP did not improve sensitivity because the staining pattern was amorphous or focally granular, and thus easily confused with nonspecific staining of mucin or intracellular or free particulate material. Reliable identification of trophozoites could be made only with coexisting cyst structures. Silver staining was more advantageous because it also identified fungal infections and was faster and more cost effective than IP.