Alleles of the var1 locus on yeast mtDNA determine the apparent size of the mitochondrial translation product, var1 polypeptide. We have analyzed most of the different var1 alleles in our collection, which number at least 15, and have developed procedures and a genetic rationale for determining their origin and predicting their behavior in crosses. The var1 alleles are characterized by two genetically defined segments, designated a and b, which can move from one var1 allele to another by asymmetric gene conversion. We show that the a segment behaves as an entity in recombination; it is either present in or absent from different var1 alleles. The b segment usually, but not always, recombines as an entity; in some cases, only portions of the b segment recombine by gene conversion. Thus, the total number of electrophoretically resolvable var1 species we observe is explained by the assortment of a, b, and partial b segments. Each segment recombines at a characteristic frequency; however, one example is presented which shows that the recipient can modulate the frequency of gene conversion. Finally, we show that, like the 21S rDNA region (omega), there is polarity of gene conversion within var1.