There are few published studies on the burden of malaria during pregnancy from areas of sub-Saharan Africa where the intensity of malarial transmission is low, and few on submicroscopic malarial infections in pregnant women. The present study was conducted in New Halfa, an area of low-intensity transmission in eastern Sudan, between August 2003 and July 2004. The main aims were to assess the prevalences of submicroscopic and multiple Plasmodium falciparum infections in pregnant women (using the P. falciparum merozoite surface protein-2 as a polymorphic marker in PCR-based assays) and to determine the effects of such infections on anaemia during pregnancy. Of the 142 pregnant women who were recruited, only 17 (11.9%) were found smear-positive for P. falciparum by microscopy. The results of the PCR-based assays revealed, however, that 40 (32%) of the 125 smear-negative women had submicroscopic P. falciparum infections. Blood samples from 32 (80%) of those with submicroscopic infections showed only the FC 27 allele (of merozoite surface protein-2), six (15%) showed only the ICI allele, and two (5%) showed both of these alleles. Although the age, parity, gestational age and haemoglobin concentrations of the women with submicroscopic P. falciparum infections were not significantly different from those of the women who were smear- and PCR-negative, such infections may have a significant impact on materno-foetal health.