This study investigated the role of enteroviruses in sepsis-like illness among neonates in Kuwait. Serum samples from 139 consecutive neonates presenting with sepsis-like illness during a three and a half-year-period whose blood cultures were negative for bacterial pathogens were tested. Enterovirus RNA was detected by single-step reverse-transcription PCR (RT-PCR). Specific genotypes were identified by direct DNA sequencing of enteroviral genome. Serotype-specific antibodies in serum samples from some selected patients were detected by virus neutralization test using coxsackievirus B types (CBVs). All 139 neonates presented with sepsis-like illness and blood samples were uniformly negative for aerobic/anaerobic bacterial cultures. Fifty-six (40%) neonates had further complications of sepsis including carditis (n = 34) and multi-organ involvement (n = 22). Enterovirus RNA was detected by RT-PCR in 34 of 139 (24%) serum samples which is among the highest frequency reported so far in non-epidemic settings. Genotyping identified CBVs as most common enteroviruses, causing 19 of 34 (56%) enteroviral sepsis episodes in neonates. Of 34 carditis cases, 18 were positive for CBVs by serotyping including all 10 enterovirus RNA-positive samples. Only one fatality was observed due to liver failure in a neonate with hepatitis. Our data showed that enteroviruses are responsible for 24% of neonatal sepsis cases due to non-bacterial causes in Kuwait. The data indicate that enteroviruses should be considered in the differential diagnosis of sepsis-like illness among neonates, particularly those with negative blood cultures for bacterial pathogens.