Aim: The aim of this paper is to analyse the procedure of diagnosing pneumonias in immunocompromised patients and to point out the importance of molecular diagnostic tests that enable the identification of pathogens causing the disease and administering adequate causal therapy accordingly. Case report: We report a case of a 64-years-old female patient presented with temperature up to 39 °C and mild cough for nine days. Patient was hospitalized in a clinic for infectious diseases. So far, the patient was controlled by hematologists due to allogenic transplantation of hematopoietic stem cells preformed because of acute myelogenous leukemia. In further diagnostic, laboratory parameters indicated acute infection and the radiogram of the lung showed pathological interstitial drawing bilaterally. Pneumonia was suspected as a most likely cause. Promptly ordered hemocultures and urinecultures were sterile, and the sputum was bacteriological and mycological negative, the patient was referred to bronchoalveolar lavage bronchoscopy. The microbiological and cytological analysis of the lavage was not specific to the etiologic diagnosis, therefore the sample was treated with polymerase chain reaction (PCR) tests for the presence of the most common respiratory pathogens, as well as on Mycobacteriumtuberculosis and Pneumocystis jirovecii. Meanwhile, a computerized high resolution tomography (HRCT) was performed, which confirmed the atypical pneumonia pattern bilaterally. After obtaining a positive PCR finding on Pneumocystis jirovecii from the bronchialveolar lavage, the patient was treated with trimethoprim-sulfomethoxazole and prednisone. Therapy was successful and patient was released in a good general condition. Conclusion: Pneumocystis jirovecii pneumonia has an average mortality of 30-50%. The patient was recovered, since the disease was diagnosed and appropriate treatment was initiated on time.