Allelic variation in the Plasmodium falciparum merozoite surface protein 1 (MSP1) gene is expressed as an association of allelic types in variable blocks. In this study, a PCR strategy that can detect 24 different MSP1 association types was used to investigate allelic variation in the MSP1 gene. We identified 236 distinct association type clones in 136 wild isolates collected from southern Vietnam, analysis of which revealed that (1) recombination between two representative allelic types in the central part of the MSP1 gene did not exist, (2) frequency distribution of MSP1 association types did not differ in different population groups, and (3) particular MSP1 association types were predominant. Statistical analysis for the association of allelic types indicated significant, nonrandom associations between blocks 4 and 6 but not between blocks 2 and 4, and 2 and 6. These results suggest that selection operates in favor of particular MSP1 association types. In addition, direct sequencing of 31 isolates confirmed reported sequence substitutions in the C-terminal 19-kDa Cys-rich region of MSP1, supporting a notion of limited variations in this region, a strong vaccine candidate molecule.