This study was undertaken to determine the antimicrobial resistance pattern and species of coagulase-negative staphylococci (CNS) isolated from the blood and skin of neonates with clinical suspicion of late-onset septicaemia (>72 h post-delivery) admitted to neonatal intensive care units, with particular reference to the phenotypic and genotypic expression of methicillin resistance. Blood culture specimens were collected by venipuncture from 660 such neonates in brain heart infusion broth. Skin swabs from axillae were obtained from 60 neonates and inoculated on mannitol salt agar. All CNS thus obtained were further identified and antibiotic sensitivity was performed according to NCCLS recommendations. PCR for the mecA gene was carried out on 54 randomly selected isolates. Staphylococcus haemolyticus was the commonest species (34 %) followed by Staphylococcus epidermidis (24 %) amongst blood isolates. All blood isolates were sensitive to glycopeptides. Resistance to penicillin and methicillin was 94 and 66 %, respectively. Similar biotypes and antimicrobial resistance patterns were observed in skin isolates. All phenotypically methicillin-resistant isolates had the mecA gene and two of the phenotypically methicillin-sensitive isolates were also positive for mecA. A PCR assay for detection of the mecA gene in CNS may be a beneficial adjunct to standard susceptibility testing for timely and reliable detection of methicillin resistance. Given the large number of methicillin-resistant CNS, inclusion of vancomycin in empiric therapy for neonates with late-onset septicaemia may be justified.