Microscopic examination does not allow differentiation of drug-resistant P. falciparum infection relapse from reinfection. However, this differential diagnosis is essential for adequate therapy. Three highly polymorphic P. falciparum genes (msp1, msp2, and glurp) and their alleles reflecting the structural state of these genes were used as genetic markers for differential diagnosis by PCR with internal primers. In 27 patients the characteristics of these alleles were identical before treatment with artersunate and during repeated manifestation of symptoms 14-28 days after the end of therapy, which attested to malaria relapses. In 24 patients the structure of these allele before mefloquine therapy and during repeated manifestation of the symptoms after 2-3 months was different, which attested to reinfection.