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The use of molecular tools with a great capacity to detect and differentiate strains of Pneumocystis has resulted: in the identification of low numbers of P. jiroveci organisms in clinically silent, colonized, immunocompromised patients and in immunocompetent persons. Considering this information, the aim of this study was to determine the prevalence of P. jiroveci carriers (subclinical infections) in Portuguese patients with pulmonary disorders and in healthy individuals. A total of 45 pulmonary specimens were collected from 45 immunocompetent adults with pulmonary disorders, and 37 oral washings from 37 healthy adults, between March 2001 and February 2004. All samples were analysed by indirect immunofluorescence with monoclonal antibodies and by amplification of the LSU mtrRNA by nested PCR. The results obtained in this study indicate that: 1) P. jiroveci is frequently detected (24.4%) in patients with pulmonary disorders in Portugal; 2) this population might play a role in circulation and transmission of P. jiroveci organisms in the community; 3) patients receiving corticosteroids are more likely to have detectable P. jiroveci in lungs (18%) than patients who are not receiving this immunosuppressor (12%); 4) P. jiroveci is infrequently detected in healthy adults. This may be due to very low numbers of latent organisms present in the lungs of healthy adults, difficulty in detecting few organisms, or due to the type of samples used. Screening of these individuals and notification of the results to their physician might be important: for further follow-up and whether or not prophylaxis or treatment should be prescribed; and for the clarification of the epidemiology of P. jiroveci asymptomatic infections.