Pneumocystis pneumonia is one of the most common pulmonary infections in patients with acquired immunodeficiency syndrome (AIDS) and in immunosuppressed organ transplant recipients. Pneumocystis jiroveci infection is acquired by inhalation of trophozoites or cysts and their subsequent development in the lungs. The cysts are thick walled, 5 to 8 μm, with round to oval and navicular boat-shaped partially collapsed cysts forms, and stain with Gomori methenamine silver (GMS), cresyl violet, and toluidine blue stains. In the vegetative forms of P. jiroveci, the trophozoites are 2 to 8 μm. They are attached to the alveolar epithelial cells and do not stain with GMS, but rather with Romanowsky stains (Giemsa, Wright, Diff-Quick). Trophozoites and cysts may be seen within the foamy alveolar exudates by using special stains.

Transbronchial biopsy is often useful in the diagnosis of pulmonary Pneumocystis infection. The presence of eosinophilic foamy or bubbly alveolar exudates in the biopsy is highly suggestive of Pneumocystis infection and should be confirmed with GMS stain. Interstitial and alveolar fibrosis with type 2 alveolar epithelial cell hyperplasia and granulomas may be seen in chronic infections. Occasionally in patients who have received treatment, cysts do not stain with GMS and are demonstrated only with immunostain.