Stenotrophomonas maltophilia infection is of concern in patients with cancer. Antibiotics active against S. maltophilia are rarely used in the treatment of febrile neutropenia, making it important to identify the factors influencing mortality in cancer patients with S. maltophilia infection. The objective of this study was to analyze the clinical characteristics and outcomes of cancer and hemopathic patients with S. maltophilia infection and assess the factors influencing the mortality. The microbiology laboratory records of Erciyes University, Faculty of Medicine Hospital were reviewed to retrospectively identify patients with S. maltophilia infection between January 2007 and June 2011. A total of 38 patients (25 male, 13 female) were eligible for the study. The median age of the patients was 53 years. The underlying disease was hematological malignancy and disorders in 76.3 % (29 cases), solid tumors in 15.8 % (six cases), aplastic anemia in 7.9 % (three cases), while 18.4 % (seven cases) were hematopoietic stem cell transplantation (HSCT) recipients. An indwelling central venous catheter was used in 32 cases (84.2 %). Twenty-seven patients (71.1 %) were neutropenic at the onset of infection. Nine patients (23.7 %) were receiving corticosteroid therapy. The overall 14-day mortality rate was 50 %. Three of the patients received empirical antibacterial treatment, and three HSCT recipients received trimethoprim-sulfamethoxazole prophylaxis, which is active against S. maltophilia. Severe sepsis (OR 13.24, 95 % confidence interval (CI) 1.62-108.57) and the duration of the treatment (OR 0.73, 95 % CI 0.60-0.90) were related to death based on logistic regression analysis findings. In immunocompromised hematology-oncology patients with severe sepsis, S. maltophilia should be considered as a possible cause of infection, and should be given effective empirical antibiotic treatment immediately; the antimicrobial spectrum may be narrowed according to results of antibiotic susceptibility test.