Abstract In this study, we present an analysis of the Plasmodium vivaxMSP-1 polymorphic region 5 and identify a new recombinant gene element. In clinical isolates from Papua New Guinea (PNG), the P. vivaxMSP-1 gene type was characterized by restriction fragment length polymorphisms and by Southern blot oligonucleotide hybridizations using probes to type-specific sequences. There were three pairs of dimorphic gene elements in the MSP-1 polymorphic region 5; four of the eight potential different combinations of sequence elements for this region have been identified. The center gene segment was the most polymorphic, especially for the glutamine (Q) repeat element with virtually every gene containing a different length of Q repeats, a finding consistent with database sequence information. The frequencies of all of the polymorphic MSP-1 gene elements were approximately equal except for the first segment, which was biased 10:1 for the Type II (Sal-1 type) versus Type I (Belem type) gene segment. In fact, only one combination (I/Q/S) of the genetic elements containing the type I gene segment for polymorphic region 5 was identified, a finding consistent with sequences reported to gene data banks. Considering only the multiplicity of MSP-1 gene types, 38% of the patients were identified as having multiple infections; when correlated with the circumsporozoite protein and the Duffy antigen binding protein gene types, the multiple infection rate increased to 65% of 23 isolates characterized. Increased age was the only clinical parameter that positively correlated with multiclonal infections and there was no other apparent bias or linkage of gene types among the three loci. These data identify multiple clonal populations of P. vivaxin the PNG population and potentially a high rate of concurrent infections in clinical cases. The extreme polymorphism of the MSP-1 polymorphic region 5 suggests that frequent recombination occurs within this gene. The bias in frequency for one recombinant gene motif indicates that intrinsic host or parasite factors may engender increased frequency of one genetic element over another. Failure to identify this type of discrete clonal marker as well as reliance on a single marker can mask the true multiclonal nature of an infection and lead to underestimation of the multiplicity of infection.