The polymorphism in nine enzyme systems in apple (Malus domestica Borkh.) was analyzed using horizontal starch gel electrophoresis. The systems studied included aspartate aminotransferase, diaphorase, glucosephosphate isomerase, isocitrate dehydrogenase, phosphoglucomutase, and triosephosphate isomerase. The products of at least 27 loci could be distinguished in these systems, 19 of which displayed polymorphism. Joint segregation analysis in populations derived from crosses between highly heterozygous cultivars revealed four multilocus linkage groups: Aat-c–Idh-1, Dia-2–Mdh-4, Gpi-c2-Aat–p, and (Dia-5, Pgm-p1)–(Mdh-2, Tpi-c2). Although several of the populations investigated had been prescreened for resistance to apple scab, cedar-apple rust, or fire blight, no correlation could be established between the inheritance of an allozyme and a resistant phenotype. The high frequency of duplicate loci encountered is in accordance with the postulated tetraploid nature of the genome.