BACKGROUND New diseases and therapies that lead to marked immunocompromise, have brought to medicine so-called opportunistic infections, caused by pathogens that usually do not cause disease in the presence of a healthy immune system. First diagnosed in AIDS patients, opportunistic infections have appeared in many other situations, including transplant recipients, other immunosuppressed patients, and even in otherwise healthy patients undergoing major elective surgery. Among the most common pathogens causing atypical infections are: Pneumocistis jiroveci, Chlamydia, Mycoplasma and Legionella. The aim of this retrospective study was to assess the incidence of the above mentioned infections in cardiac surgical patients whose early postoperative period was complicated by respiratory distress. METHODS The postoperative course of 5026 cardiac surgical patients was analysed retrospectively. In 196 cases (3.9%), important respiratory complications, defined as prolonged (>24h) requirement for mechanical ventilation, pulmonary oedema, atelectasis, pneumothorax, haemothorax, infiltrations present on chest x-ray, or ARDS, were detected. RESULTS Positive atypical sputum cultures (Chlamydia pneumoniae, Mycoplasma pneumoniae or Pneumocistis jiroveci) were obtained from 27 patients (16%). Pneumocistis jiroveci was the most common pathogen identified. Legionella pneumoniae was never cultured. The average duration of mechanical ventilation in the study group was 253 h, and the mortality 18.5% (5 patients). CONCLUSIONS Opportunistic infection with atypical pathogens should be suspected in the postoperative period when complicated by prolonged respiratory distress and difficulties with weaning from mechanical ventilation. Since these infections do not present with obvious symptoms, the diagnostic process should be extended and appropriate treatment introduced.