While methicillin-resistant Staphylococcus aureus (MRSA) isolated from urinary tract infection (UTI) has recently increased in elderly adult urology patients, it has been only rarely reported in infants. Therefore, in this study to understand whether MRSA may be involved in UTI of infants who run fever without other apparent causes, we identified and counted S. aureus and S. epidermidis in suprapubic urine from 750 febrile infants via microbiological methods, and confirmed the counts via multiplex PCR. And we also detected four virulence genes, mecA, PVL, bbp and icaA genes for S. aureus and S. epidermidis via multiplex PCR in the same specimens. S. aureus (28 cases) counts were as follows: $>10^4;CFU/ml$ (3/28), $10^2{sim}10^3;CFU/ml$ (1/28) and $<10^2{sim}10^3;CFU/ml$ (24/28). S. epidermidis (26 cases) counts were as follows: $>10^4;CFU/ml$ (2/26), $10^2{sim}10^3;CFU/ml$ (4/26) and $10^2{sim}10^3;CFU/ml$ (20/26). S. aureus virulence genes were detected in 26 cases as mecA (16/26, 59.3%), PVL (17/26, 63.0%), bbp (7/26, 26.9%) and icaA (20/26, 76.9%). S. epidermidis virulence genes were detected in 22 cases as mecA (17/22, 81.0%), PVL (15/22, 71.4%), bbp (3/22,13.6%) and icaA (13/22, 50.1%). Therefore, mecA, PVL and icaA genes of MRSA and MRSE were detected with high positivity in urines from infants with fever. The results demonstrate that community-acquired MRSA or MRSE may be responsible for UTI incidence in febrile infants.