This work was undertaken to elucidate some aspects of the epidemiology of Pneumocystis pneumonia (PP). We studied 42 mechanically ventilated, human immunodeficiency virus (HIV)-negative, severely ill neonates treated at an intensive care unit. The study group included 40 premature neonates and two mature neonates with lethal congenital defects. Progressive respiratory dysfunction in PP necessitated mechanical ventilation. Infection was usually noticeable on the 22nd day of life or after 12 days of ventilation. The usual manifestations included apnea, pallor, copious frothy sputum, seizures, and feeding difficulties. The diagnosis was established by detecting Pneumocystis jiroveci cysts in bronchial lavage fluid specimens (88.1% sensitivity). PP was managed with cotrimoxazole and pentamidine combination therapy administered over 14 days. No clinical improvement was noted in four neonates and three of them died during therapy. Prematurity and protracted mechanical ventilation are two risk factors for P. jiroveci infection in severely ill neonates in an intensive care unit.