Abstract Introduction: Pneumocystis pneumonia (PCP) is one of the most serious life threatening infections in patients with human immunodeficiency virus. It can also occur in immunosuppressed patients treated with immunosuppressive drugs.Immunocompetent adults can carryPneumocystis.The aim of this study was to identify Pneumocystis jirovecii in patients with pulmonary disorder. Materials and Methods: During 9 months (September 2014 - May 2015), 138 Bronchoalveolar Lavage (BAL) samples obtained from patients undergone bronchoscopy referred to different departments of University Hospitals of Mashhad. Giemsa stained smear and molecular method performed for each sample. After DNA extraction, amplification of mitochondrial gene coding ribosomal large subunit (mtLSU-rRNA) of P. jirovecii was performed by Nested-PCR. To reconfirm diagnosis and definite identification, gene sequencing was performed. For statistical analysis t-test and chi-square tests were used, by using SPSS version 16. Results: By direct microscopy, P.jirovecii was diagnosed in only 3(2.2%) samples, but DNA was detected in 17 (12.3%) by nested PCR. P. jirovecii isolated from 10 (25%) immunosuppressed and 7 (7.1%) of immunocompetent individuals. Fever, dyspnea and dry cough were the most common symptoms among patients with P.jirovecii. Conclusion: P. jirovecii is prevalent in immunodeficient patients compared to immunocompetent individuals. The latter group can act as reservoir of P.jirovecii and can be an important source of infection for patients with pulmonary disorders.