Objective To investigate the related clinical factors and homology of strains in Stenotrophomonas maltophilia (S. Maltophilia) infections in 15 patients with liver transplantation. Methods Fifteen patients with S. Maltophilia infection from September to December 2006 were enrolled and their clinical data were collected. Minimal inhibitory concentrations (MICs) of 10 antimierobial agents against S. Maltophilia were determined by Etest strips. Antibiogram was carried out by resistance analysis assembly with WHONET 5 software. The genomic DNA of all the isolates was digested with Xbal and subjected to pulse-field gel electrophoresis (PFGE). Results All patients received mechanical ventilation during the treatment and had a history of long-term use of extended-spectrum β-lactamases and quinolones. MICs of 10 antimicrobial agents indicated that S. Maltophilia were susceptible to several antimicrobial agents including compound sulfamethoxazole and ciprofloxacin, but the best active agent against these resistant isolates was minocycline in vitro. The results of all 15 S. Maltophilia antibiograms were accordance with PFGE patterns. All 15 S. Maltophilia isolates were classified as 2 PFGE patterns: 9 for pattern A and 6 for pattern B. Conclusion Mechanical ventilation might be associated with the S. Maltophilia septicemia in patients with liver transplantation.