OBJECTIVE: To investigate the molecular epidemiology of the penicillin-nonsusceptible Streptococcus pneumoniae (PNSP) in Beijing, China. METHODS: The resistant profile of 63 PNSP strains isolated from children with upper respiratory infection in the outpatient department from 2000 to 2002 was analyzed. The isolates were compared by detecting restriction fragment length polymorphism (RFLP) of the penicillin-binding protein (PBP) genes pbp1a, pbp2b and pbp2x and by applying chromosomal macrorestriction patterns detected by pulsed-field gel electrophoresis (PFGE). RESULTS: Sixty-one (96.8%) out of the 63 PNSP strains were multidrug-resistant Streptococcus pneumoniae (Sp). Overall, 16 resistance profiles were found, 14 of which were multidrug resistant profiles. Seven (33.3%), 6 (24.0%) and 8 (47.1%) strains resistant to one of cephalosporins were respectively isolated in 2000, 2001 and 2002, indicating an increasing trend but without any statistical significance (chi(2) = 2.42, P > 0.05). The RFLP results showed 8, 9 and 18 genotypes of pbp1a, pbp2b and pbp2x, respectively. A total of 30 patterns were found according to the three pbps types. And clearly, the most common 5 patterns had main resistant profiles. In the mean time, 35 different PFGE types were elucidated and the 9 PFGE types, with each consisting of more than 2 strains, covered 59% (37/63) of all isolates. One of the 9 PFGE type included 2 strains, both possibly related to each other, but one of them was detected to be the same PFGE pattern with clones prevalent in Asia, Vietnam-19 serogroup, Singapore-19 serogroup, Taiwan-19 serogroup, and the other was the same as that in Korea-19 serogroup. CONCLUSION: Multidrug resistance is very common among PNSP isolates in Beijing. The spread of a few multidrug resistant clones is an important factor for the prevalence of PNSP. It deserves the concern that the resistant clones spread in Asia have been found in Beijing.