Despite its limited pathogenicity, Stenotrophomonas maltophilia is an emerging nosocomial pathogen. This study investigated the isolation frequency, antimicrobial resistance and genotypic relationships of 205 S. maltophilia isolates from 188 patients in a university hospital between 1998 and 2003. Susceptibility profiles for 11 antimicrobial agents were determined by the NCCLS agar dilution method for non-fermentative bacteria, while enterobacterial repetitive intergenic consensus sequence (ERIC)-PCR and pulsed-field gel electrophoresis (PFGE) were used for genotyping of the isolates. Of the 205 isolates, 56.1% were isolated in the last 2 years of the study. The risk of S. maltophilia isolation was higher in intensive care units, S. maltophilia was isolated mostly (86.8%) after hospitalisation for >= 48 h, and 90.4% of the patients had underlying diseases. Resistance levels were > 60% for all antimicrobial agents tested except co-trimoxazole. High genetic diversity was found among the S. maltophilia isolates, and cross-infection with S. maltophilia was not common. Although ERIC-PCR revealed fewer genotypes than PFGE, it proved to be a rapid and easy method for S. maltophilia genotyping, and was more economical than PFGE.