The purpose of this study was to determine the period of persistence of Pneumocystis carinii in the lungs after P. carinii pneumonitis (PCP). After primary PCP was induced with dexamethasone, experimental rats were moved to a high-efficiency particulate air-filtered isolator to prevent further exposure to environmental P. carinii and allowed to recover. At intervals thereafter, sample groups were transferred to a second isolator and reimmunosuppressed with dexamethasone to provoke PCP if P. carinii were present. Reactivation of PCP was assessed by histologic examination, counts of cysts per gram of lung, and DNA amplification using nested polymerase chain reaction. A sequential and progressive decrease in P. carinii was detected. Thus, P. carinii is cleared from the lungs of > or = 75% of animals within 1 year after an episode of PCP, implying that persistence of latent organisms is limited.