BACKGROUND: The importance of fevers not due to malaria [non-malaria fevers, NMFs] in children in sub-Saharan Africa is increasingly being recognised. We have investigated the influence of exposure-related factors and placental malaria on the risk of non-malaria fevers among children in Kintampo, an area of Ghana with high malaria transmission. METHODS: Between 2008 and 2011, a cohort of 1855 newborns was enrolled and followed for at least 12 months. Episodes of illness were detected by passive case detection. The primary analysis covered the period from birth up to 12 months of age, with an exploratory analysis of a sub-group of children followed for up to 24 months. RESULTS: The incidence of all episodes of NMF in the first year of life (first and subsequent) was 1.60 per child-year (95 % CI 1.54, 1.66). The incidence of NMF was higher among infants with low birth weight [adjusted hazard ratio (aHR) 1.22 (95 % CI 1.04-1.42) p = 0.012], infants from households of poor socio-economic status [aHR 1.22 (95 % CI 1.02-1.46) p = 0.027] and infants living furthest from a health facility [aHR 1.20 (95 % CI 1.01-1.43) p = 0.037]. The incidence of all episodes of NMF was similar among infants born to mothers with or without placental malaria [aHR 0.97 (0.87, 1.08; p = 0.584)]. CONCLUSION: The incidence of NMF in infancy is high in the study area. The incidence of NMF is associated with low birth weight and poor socioeconomic status but not with placental malaria.