The principal objectives of this study are to (a) investigate the prevalence of elevated blood lead levels (EBLLs) in children of three major cities of Nigeria with different levels of industrial pollution; (b) identify the environmental, social and behavioral risk factors for the EBLLs in the children; and (c) explore the association between malaria (endemic in the study areas) and EBLLs in the pediatric population. The study involved 653 children aged 2-9 years (average, 3.7 years). The mean blood lead level (BLL) for the children was 8.9+/-4.8microg/dL, the median value was 7.8microg/dL, and the range was 1-52microg/dL. About 25% of the children had BLL greater than 10microg/dL. There were important differences in BLLs across the three cities, with the average value in Ibadan (9.9+/-5.2microg/dL) and Nnewi (8.3+/-3.5microg/dL) being higher than that in Port Harcourt (4.7+/-2.2micro/dL). Significant positive associations were found between BLL and a child's town of residence (p<0.001), age of the child (p=0.004), length of time the child played outside (p<0.001), presence of pets in a child's home (p=0.023), but negatively with educational level of caregiver (p<0.001). This study is one of the first to find a significant negative association between BLL and malaria in a pediatric population, and this association remained significant after controlling for confounding diseases and symptoms. The shared environmental and socio-demographic risks factors for lead exposure and Plasmodium (most common malaria parasites) infection in urban areas of Nigeria are discussed along with possible ways that lead exposure may influence the host response to infection with malarial parasites.