Abstract: A number of the stage specific antigens were used to develop the vaccines and to differentiate the strains of Plasmodium falciparum. Polymerase chain reaction amplification was used to determine polymorphisms of the genes of Merozoite Surface Protein 1 (MSP-1) and merozoite surface protein 2 (MSP-2) and as well as Circum Sporozoite Protein (CSP). A total of 67-microscopically positive Plasmodium falciparum infected individuals from a major endemic region, Southeast Iran, were included in this trial. Five fragments of MSP-1, 8 of MSP-2 and 3 of CSP were identified. The results showed that amplified products from these surface antigens varied in size and there was a specific pattern for each strain, besides, regarding this pattern 10 multiple infections with at least two clones were observed. Fragment 320 bp MSP-1 loci demonstrated high frequency in patients of more severe clinical manifestations. While the malaria endemic region of Iran is classified as low to moderate group but extensive polymorphisms was observed for each marker and the MSP-2 central repeat was the most diverse one.