Malaria is thought to be rare among neonates in malaria-endemic regions. Consequently, blood film for malaria parasite is not routinely included in the sepsis screening protocol for neonates. We examined the role of malaria in perinatal morbidity among neonates admitted into our unit with a view to determining the need or otherwise of including malaria parasitaemia in the sepsis work-up in suspected neonatal septicaemia. Fourteen babies who met our preset criteria were screened for malaria parasitaemia out of which five (35.71 per cent) had positive blood smears for Plasmodium falciparum. Eighty per cent of the neonates presenting with fever had positive blood films (Yates corrected chi2 = 3.9822; p = 0.04). All the babies responded to an oral course of chloroquine. These data have further highlighted the importance of malaria in perinatal morbidity in our environment. We recommend a multi-centred study to define clearly the role of malaria in perinatal and neonatal morbidity and mortality in malaria endemic areas.