As alternative regimens in therapy of Stenotrophomonas maltophilia infections are limited, epidemiological investigation of S. maltophilia is necessary for developing new strategies in prophylaxis of these infections. "Enterobacterial repetetive intergenic consensus-polymerase chain reaction (ERIC-PCR)", is a simple and rapid method to detect the genomic polymorphism at the strain level in nosocomial outbreaks due to S. maltophilia. The aim of this study was to investigate the molecular epidemiology of S. maltophilia strains isolated from paediatric patients in a university hospital. A total of 40 clinical isolates one from each of 35 patients, two pairs from two patients and one from an environmental source, were collected between 1998-2001 period. Susceptibility to eleven antimicrobials was studied by agar dilution test according to NCCLS criteria. Resistance rates of the tested isolates against piperacillin, piperacillin-tazobactam, ceftriaxone, ceftazidime, cefepime, ciprofloxacin, imipenem, meropenem, amikacin, gentamicin and trimethoprim-sulfamethoxazole were 57.5%, 25%, 85%, 37.5%, 47.5%, 20%, 100%, 95%, 62.5%, 62.5% and 5%, respectively. Trimethoprim-sulfamethoxazole was the most active agent against the tested isolates. The isolates were analyzed by ERIC-PCR by using each of ERIC-I and ERIC-II primers. Genotypic analysis by ERIC-PCR identified 24 different major and 4 minor profiles. Three isolates from each of four different groups, two isolates from each of other four different groups were unique. The results of this study, revealing a great genomic diversity and low clonality within the strains of S. maltophilia strains suggest that patients may be colonized with the naturally occuring isolates in the hospital environment and then get infected with these strains under the selective antibiotic pressure, thus supporting the view that clonal spread of S. maltophilia strains between patients is of rather low possibility.