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<p>Abstract</p> <p>Background</p> <p>Rapid diagnostic tests (RDTs) have revolutionized the diagnosis of malaria. Among the various factors affecting RDTs sensitivity is genetic variation of the antigen used. The genetic variation in PfHRP2 and PfHRP3 proteins was studied among the Indian <it>Plasmodium falciparum</it> isolates.</p> <p>Methods</p> <p>One hundred and forty isolates of <it>P. falciparum</it> were collected from six geographical regions of India. Target genes encoding PfHRP2 and PfHRP3 antigens were sequenced to study genetic polymorphism. Minimum detection limit giving a positive rapid diagnostic test was also determined.</p> <p>Results</p> <p>Extensive variations were observed in amino acid repeat types of PfHRP2 and PfHRP3. PfHRP2 exhibited more polymorphism than PfHRP3. Significant relation was observed between type 2 and type 7 repeats and RDT detection rate as higher number of these repeats showed better sensitivity with RDTs.</p> <p>Conclusion</p> <p>The results provide insights into the genetic diversity of <it>Pfhrp2</it> and <it>Pfhrp3</it> genes among Indian <it>P. falciparum</it> population and its relation to RDT sensitivity.</p>