Background: Malaria adversely affects pregnant women and their fetuses or neonates. Estimates of the malaria burden in pregnant women based on health facilities often do not present a true picture of the problem due to the low proportion of women delivering at these facilities in malaria-endemic regions. Methods: Data for this study were obtained from the Healthy Beginning Initiative using community-based sampling. Self-identified pregnant women between the ages of 17-45 years were recruited from churches in Enugu State, Nigeria. Malaria parasitaemia was classified as high and low based on the malaria plus system. Results: Of the 2069 pregnant women for whom malaria parasitaemia levels were recorded, over 99 % tested positive for malaria parasitaemia, 62 % showed low parasitaemia and 38 % high parasitaemia. After controlling for confounding variables, odds for high parasitaemia were lower among those who had more people in the household (for every one person increase in a household, OR = 0.94, 95 % CI 0.89-0.99). Conclusion: Results of this study are consistent with hospital-based estimates of malaria during pregnancy in southeastern Nigeria. Based on the high prevalence of malaria parasitaemia in this sample, education on best practices to prevent malaria during pregnancy, and resources in support of these practices are urgently needed.