PCP is diagnosed by using a microscope to identify P. jirovecii organisms in a sample of lung fluid or tissue. The sample is usually induced sputum or bronchoalveolar lavage (BAL) material. It may be necessary to get the sample through transbronchial biopsy or open-lung biopsy – these diagnostic techniques are more sensitive and specific, but they are also more invasive.
Polymerase chain reaction (PCR) is also used to detect P. jirovecii DNA in clinical specimens. PCR can be particularly helpful in detecting silent P. jirovecii infections in HIV-infected patients.