P. carinii, the cause of PCP, usually is classified as a protozoan, although some investigators consider it more closely related to fungi. The organism exists as a saprophyte in the lungs of humans and various animals.

Part of the normal flora in most healthy people, P. carinii becomes an aggressive pathogen in the immunocompromised patient. Impaired cell-mediated (T-cell) immunity is thought to be more important than impaired humoral (B-cell) immunity in predisposing the patient to PCP; however, the immune defects involved are poorly understood.

The organism invades the lungs bilaterally and multiplies extracellularly. As the infestation grows, alveoli fill with organisms and exudate, impairing gas exchange. The alveoli hypertrophy and thicken progressively, eventually leading to extensive consolidation.

The primary transmission route seems to be air, although the organism is already resident in most people. The incubation period probably lasts 4 to 8 weeks.

The patient typically has a history of an immunocompromising condition (such as HIV infection, leukemia, or lymphoma) or procedure (such as organ transplantation).