Pneumocystis pneumonia (PCP) is a potentially life-threatening infection for the immunocompromized patients. However, Pneumocystis jirovecii colonization can also be detected in healthy individuals and in patients with various underlying lung diseases. The aim of this study was to evaluate the immunocompetent and iatrogenically immunosuppressed patients in terms of PCP and P.jirovedi colonization. A total of 92 patients (66 male, 26 female; age range: 18-93 years, median: 58.5) who underwent bronchoscopy due to various pulmonary symptoms between January 2011-April 2014, were included in the study. Of these patients, 65 were under immunosuppressive therapy (38 were treated with anti-cancer drugs, 15 with anti-rejection/immunomodulatory drugs and 12 with corticosteroids), while 27 were immunocompetent. Bronchoalveolar lavage (BAL) fluids were evaluated for the presence of P.jirovedi mitochondrial gene coding ribosomal large subunit (mtLSUrRNA) with nested PCR (nPCR) method. All of the samples were also examined by Giemsa and Gomori's methenamine silver (CMC) staining methods. P.jirovedi DNA was detected in 31 (33.7%) out of 92 BAL samples by nPCR. Although six immunosuppressed patients were positive in the first round of amplification, 26 of 65 (40%) immunosuppressed and five of 27 (18.5%) immunocompetent patients were positive with nPCR. P.jirovedi cysts and trophozoites were detected in only five (16.1 %) of the 31 nPCR positive samples. The probability of being immunosuppressive among nPCR positive cases was statistically higher than nPCR negative cases (Χ2= 3.940; p= 0.047). This difference was more significant in organ transplant recipients and patients under anti-rejection/immunomodulatory treatment (Χ2= 6.715, p= 0.01; Χ2= 5.550, p= 0.018, respectively). When clinical, laboratory and radiological findings of nPCR positive patients were considered, five patients (2 kidney transplant, 1 bone marrow transplant, 1 interstitial lung disease and 1 lung cancer case) in immunosuppressed group were interpreted as "definite PCP" and eight patients (2 kidney transplant, 1 leukemia, 1 connective tissue disease, 1 Wegener's granulomatosus, 2 rheumatoid arthritis and 1 lung cancer case) were interpreted as "probable PCP". Other 18 (19.6%) nPCR positive patients, of them 13 were immunosuppressive and five were immunocompetent, were considered as "P.jirovedi colonization". The colonization rate was determined as 50% (13/26) in immunosuppressive patients, and was mostly detected in patients with hematological malignancies (4/13), followed by patients with solid tumors (3/13) and organ transplantations (3/13). On the other hand, all of the nPCR positive immunocompetent patients (5/5) were evaluated as colonization. In this study significant data was obtained about P.jirovedi epidemiology in our country. Our results also showed that iatrogenically immunosuppressed patients are under risk of PCP and nPCR method is more sensitive than conventional PCR and classical staining methods in the diagnosis of these patients.