Stenotrophomonas maltophilia (SM) is an important nosocomial pathogen. Due to its intrinsic resistance to various therapeutic drugs, the optimal antimicrobial therapy is often delayed. From January 2005 to September 2012, we retrospectively compared drug susceptibilities, clinical backgrounds, and outcome of SM bacteremic patients (SM group) with these of other non fermentative gram negative bacilli bacteremic patients (non-SM group), at a tertiary-care hospital in Kyoto, Japan. Among the SM group, risk factors of 30-day mortality were evaluated. The SM group and non-SM group included 54 and 237 cases, respectively. Among the non-SM group, bacteremic patients due to Pseudomonas aeruginosa, Acinetobacter species, and other non-fermentative gram negative bacilli included 156, 68, and 13 patients, respectively. SM isolates were susceptible to trimethoprim-sulfamethoxazole and minocycline (82.0% and 100%, respectively). Non-SM isolates were susceptible to meropenem (88.6%), ceftazidime (88.6%), cefepime (85.2%), and amikacin (97.0%). Both SM and non-SM isolates were susceptible to levofloxacin (87.5% and 82.0%, respectively). The use of carbapenems, antipseudomonal cephalosporins, and isolation of SM within 30 days represented an independent risk factor for SM bacteremia. The 30 day mortality rate among the SM group was significantly higher compared with the non-SM group (35% vs 18%, odds ratio: 2.2, 95% CI: 1.2-4.3 p = 0.012). Among the SM group, an independent factor which was associated with 30-day mortality was the SOFA score. SM bacteremia showed a worse outcome compared with bacteremia due to non-SM. For the patients who present risk factors for SM bacteremia, empirical antimicrobial therapy including trimethoprim-sulfamethoxazole, minocycline or levofloxacin should be considered.