A total of 29 meticillin-resistant Staphylococcus aureus (MRSA) isolates were obtained from 15 neonates and three healthcare workers (HCWs) in a neonatal intensive care unit (NICU) and special care baby unit (SCBU) and four patients in a medical ward of a Kuwait hospital between 10 and 30 April 2007. The isolates were characterized using antibiogram results, coagulase gene RFLP (coa-RFLP), PFGE, staphylococcal cassette chromosome mec (SCCmec) typing and multilocus sequence typing (MLST). All isolates were assessed for the carriage of Panton-Valentine leukocidin (PVL) and arginine catabolic mobile element (ACME) genes. The isolates belonged to three SCCmec types, six coa-RFLP types, six pulsotypes and six sequence types. One isolate was positive for PVL. None were positive for ACME. All MRSA isolates from the 15 neonates were phenotypically and genetically different from the MRSA isolates obtained from HCWs and those from patients in other wards. They were resistant to gentamicin, kanamycin and fusidic acid, had identical coa-RFLP and PFGE patterns, carried the type V SCCmec element and belonged to MLST sequence type ST97. The results showed the transmission of a rare clone of community-associated MRSA belonging to ST97 with the SCCmec-V genotype among neonates in a NICU and SCBU.