BackgroundThere are few published studies on Plasmodium falciparum genotypes in peripheral, placental and umbilical cord blood in areas characterised by unstable malaria transmission.MethodA cross-sectional study was conducted to investigate P. falciparum genotypes in matched peripheral, placental and umbilical cord blood in eastern Sudan. Thick blood smears and P. falciparum merozoite surface protein 1 (MSP1) and 2 (MSP2) genes as polymorphic markers in polymerase chain reactions were investigated in 3 kinds of samples of 153 pregnant women at delivery.ResultsThere was no significant difference in the prevalence of blood film-detected P. falciparum in which 5 (3.3%), 7 (4.6%) and 3 (2.0%) (P = 0.437) of the 153 samples were determined to be P. falciparum-positive by microscopy for maternal peripheral, placental and cord blood samples, respectively.Out of these 145 samples, 24 (16.6%), 39 (26.9%) and 24 (16.6%) (P = 0.039) of the peripheral, placental and cord samples, respectively, had submicroscopic parasitaemia (blood films were negative). There was no association between submicroscopic parasitaemia and age or parity.RO33 and K1 (MSP1 alleles) were detected in 21/29 (72.4%), 42/46 (85.7%), 26/27 (92.2%) and 6/29 (20.6), 16/46 (32.6) and 0(0) (P < 0.001) of the maternal, placental and cord samples, respectively. MAD20 was not detected in any of the samples.While the 3D7/IC1 allele was detected in 12 (41.3%), 30 (65.2%) and 4 (14.8%) (P < 0.001) of the peripheral, placental and cord samples, respectively, the FC (MSP2) allele was detected in only the 6 (20.6) placental samples. Multi-clonal infection was detected in 10 (34.4), 27 (58.6) and 3 (11.1) (P < 0.001) of the maternal placental and cord samples, respectively.ConclusionCompared with the peripheral and cord samples, placental samples had a higher prevalence of submicroscopic parasitaemia. MSP1 alleles were predominant in the cord, while MSP2 alleles were predominant in the placental samples, which had a significant higher multiplicity of the infection.