Efficient methods for the detection of mutations are of fundamental importance in research and in diagnostics. By detection of a DNA sequence alteration that cosegregates with a clinical phenotype in an affected family, the gene at fault may be identified and assigned a function. Mutation detection methods are also a rate-limiting factor for the clinical application of DNA diagnostics. Currently a large number of techniques are in use to scan for new mutations and to distinguish among previously established sequence variants. Here, some of the problems connected with mutation detection are discussed together with principles on which current and future mutation detection assays can be based.