In this prospective study, the risk factors associated with nosocomial sepsis Caused by Acinetobacter baumannii or Pseudomonas aeruginosa were compared. Prior use of broad-spectrum antibiotics, urinary tract catheter, prior surgery, and mechanical ventilation were significantly associated with nosocomial sepsis caused by Acinetobacter baumannii. The mean prognostic factors significantly associated with mortality were known focus of infection, multiresistant Acinetobacter baumannii, and inappropriate antibiotic treatment. Adequate knowledge of these findings is important to ensure appropriate management of patients and rational use of antibiotics.