Plasmodium falciparum resistance to chloroquine first arose in Africa 25 years ago. Nowadays most of African malaria control programmes have switched their first-line treatment of uncomplicated malaria cases towards artemisinin derivatives combination. After WHO guidelines, a survey network for malaria treatment resistance has been set up in the Niger valley around Niamey since December 2004. The association of the Niger national malaria control programme with the CERMES research center allowed collecting of samples from both health centers and hospitals of this region. Blood finger-pricks on filter papers were tested for detection of plasmodial antigen in health center without biological diagnosis capacity. Specimens found positive either in hospital laboratory or by using antigen method were tested by PCR/RFLP to detect K76T mutations on the pfcrt gene and S108N mutation on the pfdhfr gene. This simple procedure allows the screening of a large number of specimens. Moreover, a spatial distribution of mutations and evidence of resistance clusters were searched integrating the data in a geographic information system. The 76T mutation of pfcrt and 108N of pfdhfr were respectively found in 50.8% and 57% of the specimens tested. No statistically significant difference was found according to the level of sanitary formations or the age of the patients. No resistance cluster was identified and the prevalence of mutation seems homogeneous in the zone. By completing the clinical efficacy studies we think that our simple method for collecting and testing blood samples associated with clinical efficacy studies may be useful for building a network of malaria drug resistance in Africa.