Malaria transmission is high and perennial in south-east Nigeria and is associated with a high burden of morbidity and mortality in children under 5 years and pregnant women. It is associated with maternal anemia, placental infection, intrauterine growth retardation and low birth weight. To evaluate the status of malaria in pregnancy in Cross River State, Nigeria, we assessed the prevalence rates of maternal, cord and placental malaria parasitemia in the dry and rainy seasons for 626 consecutively recruited pregnant women who delivered at two rural and two urban health facilities. Demographic data were obtained at delivery and maternal, placental and cord blood samples were collected and examined for malaria parasites by light microscopy. Of the mother and infant pairs, 120 (19.2%), 69 (14.7%) and 62 (13.5%), respectively, had positive maternal, placental and cord blood parasitemia. Parasitemia rates in the rainy season were higher than in the dry season (p < 0.05). There were no significant differences in maternal, placental and cord parasitemia between urban and rural areas. The prevalence rates of parasitemia at delivery indicate high malaria transmission and poor control during pregnancy.