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We observed an atypical Pneumocystis infection with spontaneous pneumothorax, bronchopleural fistulae, an apical cyst and Pneumocystis pleuritis after aerosolized pentamidine prophylaxis in an AIDS patient. These findings suggest a failure of pentamidine aerosol in controlling active Pneumocystis infection in peripheral pulmonary areas. A relapse of Pneumocystis carinii pneumonia (PCP) must be suspected when pneumothorax occurs during secondary prophylaxis with aerosolized pentamidine. It should always be confirmed by bronchoalveolar lavage or transbronchial or open biopsy. Cases presenting as atypical Pneumocystis pneumonia may additionally reveal extrapulmonary dissemination of Pneumocystis infection.