Background: Treatment failure in clinical trial, may be caused by P. falciparum resistant to antimalarialdrug. This study aimed to confirm the treatment failure cases of P. falciparum whcther caused byrecrudescence / resistant or new infection of different strain parasite.Methods: This study was a part of the activity in antimalarial drug efficacy trials (artemisinin-naphthoquine/AN versus dihydroartemisinin – piperaquine/DHP). P. falciparum infections on failure cases weregenotyped for allelic variation in those 3 markers by comparing before (D0) and after treatment (DF) ifparasites recurrent with nested polymerase change reaction (PCR).Results: Thirteen of 19 P. falciparum failure cases showed PCR genotyping completely successful 100%for MSP1 (D0 & DF), MSP2 (DF) and GLURP (D0) and the lowest (76,9% ) for GLURP (DF). Whenall 3 genes were combined, the amplification result showed 69.2%. Identification allele for each locusgenes shown that MSP1 had just one (D0 or DF). Conversely, for MSP2 and GLURP, there were someadditional alleles either at D0 and DF. By comparing the pattern of genotype (alleles) P. falciparum atD0 and DF each locus genes, the confirmation of P. falciparum resistant from new infection could bedetermined The proportion of recrudescence and new infection almost the same, 8 of 13 failed cases werefrom artemisinin-naphthoquine (AN) group.Conclusion: The confirmation of P. falciparum by comparing genotype at D0 and DF could determine parasiteresistant and new infection from treatment failure cases. Recrudescence occurred within 17 days after treatmentand new infection occurred >28 days after treatment. (Health Journal of Indonesia. 2015;6:29-37)