The Mendelian analysis of genetic variation, available as induced mutants or as natural variation, requires a number of steps that are described in this chapter. These include the determination of the number of genes involved in the observed trait's variation, the determination of dominance relationships between alleles of the same locus, and epistatic interactions with related genetic variants. A new variant should be compared with previously identified genetic variants, which is most efficiently done by allelism tests in case of recessive mutants. In addition the locus should be localized on the genetic and physical map by linkage analysis. The mapping of mutant loci in Arabidopsis is facilitated by the genomic resources available in Arabidopsis and often consists of two steps, a crude and a fine mapping, the latter enabling the approximate location of a variant on the sequence map of Arabidopsis.