In 1999, following high treatment failure rates of chloroquine, the Ethiopian Ministry of Health gave directives for the use of Sulfadoxine/pyrimethamine (SP) as first line drug for the treatment of uncomplicated falciparum malaria. In 2004, this decision was altered due to high treatement failure of SP and Arthemether-Lumfantrine (Coartem®rnPfdhfr; Pfdhps; dot blot hybridization; Ethiopia ) was introduced. The study investigated the impact of withdrawal of SP on the change in frequency of SP resistance-related haplotypes in Pfdhfr (codons 51, 59 and 108) and Pfdhps (codons 437 and 540) genes by PCR based dot blot hybridization. Plasmodium falciparum positive blood samples were collected from a total of 159 patients during two cross sectional surveys in 2005 (N=80) and 2007/08 (N=79) from Pawe, North Western Ethiopia. It was determined that the frequency of SP resistance associated triple mutant Pfdhfr haplotype decreased significantly from 50.79% to 15.87% (P0.05) both of which showed that the prevalence of mutatnt alleles that cofer drug resistance are decreasing in the absence of drug pressure. The combined Pfdhfr/Pfdhps quintuple mutant haplotype that has been previously recognized to be the most important determinant of SP resistance was significantly decreased from 40.68% to 13.56% (P