We have used four gene probes specific for mouse chromosome 8, including adenine phosphoribosyltransferase (aprt), to demonstrate that the P19 teratocarcinoma stem cell line contains two distinct chromosome 8 homologs. One represents the common laboratory mouse C3H (Mus musculus domesticus) homolog while the second homolog was presumably contributed by a feral Mus musculus musculus animal. Six cell lines with APRT heterozygous deficiencies were isolated from P19 subclones. A molecular analysis of these heterozygotes demonstrated that three arose by deletion of the Mus musculus musculus aprt allele and three arose by aprt gene inactivation. APRT homozygous deficient cell lines were isolated from both classes of heterozygote; most contained little or no detectable APRT activity. When the heterozygous deficiency was due to deletion of the Mus musculus musculus aprt allele, the most frequent event yielding homozygous deficient cell lines was associated with loss of heterozygosity for all tested markers on the Mus musculus domesticus homolog indicating chromosome loss. In contrast, when the initial event resulting in APRT heterozygous deficiency was gene inactivation, homozygotes arose predominantly from gene deletion or a second inactivation event. These results suggest a potential relationship between the first- and second-step events resulting in APRT deficiencies.