Background: Malaria is more common in pregnant than in non-pregnant Nigerian women, and is associated with small birth size and the attendant short- and long-term health risks. The influence of malaria on maternal metabolic status in pregnancy and in cord blood and how this relates to birth size has not been studied. The study objective was to define relationships between maternal and cord serum metabolic markers, maternal malaria status and birth size. Methods. During pregnancy, anthropometric measurements, blood film for malaria parasites and assays for lipids, glucose, insulin and TNF were obtained from 467 mothers and these analytes and insulin-like growth factor-I (IGF-I) were obtained from cord blood of 187 babies. Results: Overall prevalence of maternal malaria was 52%, associated with younger age, anaemia and smaller infant birth size. Mothers with malaria had significantly lower cholesterol (total, HDL and LDL) and higher TNF, but no difference in triglyceride. In contrast, there was no effect of maternal malaria on cord blood lipids, but the median (range) cord IGF-I was significantly lower in babies whose mothers had malaria: 60.4 (24,145)μg/L, versus no malaria: 76.5 (24, 150)μg/L, p = 0.03. On regression analysis, the key determinants of birth weight included maternal total cholesterol, malarial status and cord insulin and IGF-I. Conclusions: Malaria in pregnancy was common and associated with reduced birth size, lower maternal lipids and higher TNF. In the setting of endemic malaria, maternal total cholesterol during pregnancy and cord blood insulin and IGF-I levels are potential biomarkers of foetal growth and birth size. © 2012 Ayoola et al; licensee BioMed Central Ltd.