A cross-sectional study was conducted in a malaria hyperendemic state of India to ascertain the distribution of Plasmodium falciparum genotypes in patients with mild (n=40) and severe (n=35) malaria. PCR and nested PCR were used to determine the glutamate-rich protein (GLURP), merozoite surface proteins 1 and 2 (MSP1 and MSP2) and knob-associated histidine-rich protein (KAHRP) for characterization of the parasite. The results indicate that (i) the 200bp allele of the MAD20 family of MSP1 and the 550bp allele of the 3D7 family of MSP2 show over-representation in severe malaria cases; (ii) the multiplicity of infection with respect to MSP2 alleles is significantly higher (P<0.001) in severe cases than in mild cases; and (iii) comparison with the findings of other studies leads to the conclusion that the distribution of P. falciparum genotypes between different clinical groups differs geographically.