Fragment size in the Block 2 repetitive region of merozoite surface protein 1 (MSP1) has commonly been used as a molecular marker in studies of malaria transmission dynamics and host immunity in Plasmodium falciparum malaria. In this study, we further explore the genetic variation in MSP-1 Block 2 underlying potential problems faced while studying the immune responses elicited by this vaccine target and while using it as a molecular marker in epidemiologic investigations. We describe the distribution of a new Block 2 recombinant allele family in samples collected from western Kenya and other malarious regions of the world and provide evidence that this allele family is found worldwide and that all MR alleles most likely originated from a single recombination event. We test whether the number of tandem repeats (i.e. fragment size) can be considered neutral in an area of high transmission in western Kenya. In addition, we investigate the validity of the assumption that Block 2 alleles of the same size and allele family are identical by examining MSP1 Block 2 amino acid sequences obtained from full-length MSP-1 clones generated from infected Kenyan children and find that this assumption does not hold. We conclude that the worldwide presence of a new allele family, the effect of positive natural selection, and the lack of conserved amino acid motifs within alleles of the same size suggest a higher level of complexity that may hamper our ability to elucidate allele family specific immune responses elicited by this vaccine target and its overall use as genetic marker in other types of epidemiologic investigations.