The MSP-1 gene from the rodent malaria parasite P. berghei was cloned and sequenced. PbMSP-1 exhibits the greatest sequence homology with other rodent Plasmodium MSP-1 genes. The heterogeneity between rodent Plasmodium MSP-1 sequences is evident as four variable blocks distributed within five conserved regions. Proteolytic processing sites are located at the boundaries between the conserved and variable regions and are maintained across species. Between species, there is virtually no amino acid sequence homology within the variable regions. However, the amino acid compositions are similar, implying some selective pressure at the protein level. This may be indicative of a functional role for the variable blocks. The variable regions are probably exposed on the exterior surface of the protein as random-coiled loops. Prior to terminal merozoite differentiation and release, proteolysis occurs at the processing sites adjacent to the variable regions. Proteolytic cleavage may result in extension of the variable regions, increasing their surface area as the loops take on a less constrained conformation. The resulting projections may facilitate interactions between the merozoite and potential host cells Intraspecies sequence heterogeneity within the variable regions was also assessed among several P. berghei lines. Tandem repeats are observed in all four variable blocks of MSP-1 from rodent parasites. Intraspecies heterogeneity in PbMSP-1 is primarily due to differences in the number of repeat units. The observation that PbMSP-1 tandem repeats are less degenerate than those found in other Plasmodium species, suggests a homogenizing mechanism acting at the level of the DNA, or that divergence within PbMSP-1 may occur at a slower rate. Nonetheless, the inherent instability of tandem repeats provides a means for generating diversity in Plasmodium antigens. The diverse tandem repeats within the variable regions would seem to contradict the assertion that these regions may play a functional role in host-parasite interactions. However, while mutational events within the MSP-1 variable blocks generate antigenically diverse regions, the amino acid compositions and random-coil structure are maintained. Thus, the requirement to maintain protein structure and presumably function is balanced with the generation of diversity