Molecular variation is widespread in parasite populations, and its analysis has important implications for studying aspects relating to the function and organisation of genes, and the taxonomy, phylogeny and population genetics of parasites. This article reviews some PCR-based mutation scanning techniques that have advantages over currently used DNA methods for the analysis of genetic variation in parasites. The review is technical and describes briefly the principles of relevant techniques, examines some of their advantages and disadvantages and gives several examples for possible applications.