Thick and thin blood films were stained with Giemsa stain (3%) for 45 minutes. Asexual parasites and gametocytes of P. falciparum were counted against 400 white blood cells. For molecular biology analyses, DNA was extracted from pre, post-treatment and cross-sectional survey filter paper blood spots using chelex. DNA was amplified by nested PCR to detect mutations at pfcrt-76. Nest 2 PCR products were digested by Apo I endonuclease restriction enzyme and electrophoresed onto a 3% agarose. Sequence-specific oligonucleotide probing (SSOP) was performed to detect the presence of pfmdr1-86 mutation. Mutations at dhfr (51, 59 and 108) and at dhps ( 437 and 540) were also detected by SSOP. MSP2 gene polymorphisms were studied by PCR to differentiate recrudescence from new infections.