<p>Abstract</p> <p>Background</p> <p>Malaria is still a public health problem in Malaysia especially in the interior parts of Peninsular Malaysia and the states of Sabah and Sarawak (East Malaysia). This is the first study on the genetic diversity and genotype multiplicity of <it>Plasmodium falciparum </it>in Malaysia.</p> <p>Methods</p> <p>Seventy-five <it>P. falciparum </it>isolates were genotyped by using nested-PCR of <it>MSP-1 </it>(block 2) and <it>MSP-2 </it>(block 3).</p> <p>Results</p> <p><it>MSP-1 </it>and <it>MSP-2 </it>allelic families were identified in 65 blood samples. RO33 was the predominant <it>MSP-1 </it>allelic family identified in 80.0% (52/65) of the samples while K1 family had the least frequency. Of the <it>MSP-2 </it>allelic families, 3D7 showed higher frequency (76.0%) compared to FC27 (20.0%). The multiplicity of <it>P. falciparum </it>infection (MOI) was 1.37 and 1.20 for <it>MSP-1 </it>and <it>MSP-2</it>, respectively. A total of seven alleles were detected; of which three <it>MSP-1 </it>allelic families (RO33, MAD20 and K1) were monomorphic in terms of size while <it>MSP-2 </it>alleles were polymorphic (two 3D7 and two FC27). Heterozygosity (H<sub>E</sub>) was 0.57 and 0.55 for <it>MSP-1 </it>and <it>MSP-2</it>, respectively.</p> <p>Conclusions</p> <p>The study showed that the MOI of <it>P. falciparum </it>is low, reflected the low intensity of malaria transmission in Pahang, Malaysia; RO33 and 3D7 were the most predominant circulating allelic families. The findings showed that <it>P. falciparum </it>has low allelic diversity with a high frequency of alleles. As a result, antimalarial drug efficacy trials based on MSP genotyping should be carefully interpreted.</p
