The main purpose of the study was to compare the in vitro sensitivity results obtained from the two widely-used in vitro systems: (1) standard WHO micro-technique based on schizont maturation inhibition using fresh isolates (M-I), and (2) micro-technique based on incorporation of [3H]- hypoxanthine using culture-adapted isolates (M-II). The study was conducted during 1998 and 2002. A total of 473 Plasmodium falciparum isolates were collected from five highly malaria endemic areas of Thailand, ie, Mae Sot district, Tak (north-western), Kanchanaburi (western), Ranong (south-western), Ratchaburi (south-western) and Chantaburi (eastern) Provinces. The antimalarials tested were: mefloquine, quinine, chloroquine, artemisinin and dihydroartemisinin. The sensitivity results for mefloquine obtained from the two methods were significantly different from each other. The IC50 values for M-II was less than M-I. The median (95%C.I.) IC50 value for mefloquine using the M-II method was significantly lower [696.47 (393.11-1,233.2) nM] than for M-I [3,955.4 (1,035.61-5,108.9) nM]. The in vitro sensitivity results for quinine were significantly different from each other. The median (95% C.I.) IC50 value for M-II [161 (42-351) nM] was 2.5-fold that of M-I [66 (24-450) nM].