Invasive procedures and antibiotic treatment increase the risk of nosocomial infections in neonatal intensive care units. Early identification and appropriate treatment is important. Herein we report two cases of massive hemorrhagic pneumonia caused by Stenotrophomonas maltophilia. The first case was diagnosed with congenital pneumonia; a chest tube was inserted because of pneumothorax on the third day of life. The second case had been referred with respiratory distress syndrome, and bilateral pneumothorax was present on admission. Upon follow up, the cases' clinical condition worsened; acute respiratory distress syndrome and massive pulmonary haemorrhage developed. After Stenotrophomonas maltophilia was isolated in blood cultures, the cases were treated successfully using a combination of trimethoprim/sulfamethoxazole and fluoroquinolone.