Summary In malaria-endemic regions, pregnant women are more susceptible to malarial infections than non-pregnant women. The main objective of this study, which was conducted in the malaria hyperendemic town of Lambaréné (Gabon, Central Africa), was to characterize Plasmodium falciparum infections in peripheral, placental and cord blood from women of different gravidities with submicroscopic infections. Using the P. falciparum merozoite surface protein 2 (MSP 2)* gene as a polymorphic marker in polymerase chain reactions, we analysed genetic diversity and multiplicity of infection in isolates from all three kinds of samples of 184 pregnant women at delivery. We detected infection in 44% of the women who were originally negative by microscopy. Equally important was the finding that the placenta had the highest prevalence of infection (P < 0.001). There was no correlation with gravidity status or age of the patients. The multiplicities of infection in the peripheral and placental blood samples did not differ and single infection was observed in cord blood, independently of the gravidity. The FC27/MSP 2 was the predominant allelic family. The major FC27 alleles detected in the peripheral, placental and cord blood were sequenced and found to be closely related to the published K1 form sequence. Below microscopy level, the placenta remains the most infected organ and this submicroscopic carriage of parasites may contribute to the development and maintenance of immunity to malaria during pregnancy.