We have compared Southern blots of rat hepatoma DNA probed with Types I, II and III hexokinase cDNAs isolated from normal rat tissues. Hybridization patterns show several fragments recognized by both the Type I and II clones while no resemblance is observed between the Type III probe and the other two isozymes. It therefore appears that the Type I-like and Type II-like hepatoma isozymes are coded for by similar yet separate genes, while a dissimilar third gene codes for the Type III-like isozyme. In addition, a loss of heterozygosity was detected at the Type III locus in the AS-30D hepatoma when compared to normal tissue. As only the Type II-like isozyme is highly expressed in highly glycolytic tumors, these data have implications for differential gene regulation between the tumor isozymes.