Although the importance of the transcription factor Pax3 has been identified in many embryological processes including neural crest cell migration, neural tube closure, and limb muscle formation, its role in proper formation of the ribs has not been well characterized. We have used the Splotch mouse which has a mutation in the Pax3 gene to determine what role Pax3 may play in rib morphogenesis. Homozygous Splotch embryos collected from days 13.5 to 16.5 of gestation displayed severe rib abnormalities including fusions at both the proximal and distal regions. Given its expression in the dermomyotome, we sought to determine when Pax3 expression in the Splotch mutant initially becomes abnormal and which rib segment progenitors may be affected. Prior to somite differentiation at 9.5 dpc (days post coitum), Pax3 is normally expressed in the somites; after differentiation, however, Pax3 expression is diminished in Splotch embryos. We also determined that significantly increased levels of apoptosis occur in the thoracic region by 11.0 dpc relative to wild-type littermates. Because Patch mouse mutants which fail to express PDGF alpha-receptor also have rib abnormalities, we sought to determine whether Pax3 may influence the expression of this receptor. By in situ hybridization, we determined that initially the expression of PDGFRalpha is normal in Splotch mutants at 10.0 dpc, but decreases by 12.5 dpc in the thoracic somite region, suggesting that Pax3 may act upstream of PDGFRalpha. Taken together, our results show that Pax3 expression is important for normal rib development and that increased apoptosis occurs in the thoracic muscles. We suggest that Pax3 may influence the expression of PDGFRalpha, and that the reduced and/or deficient thoracic muscles may contribute to the resulting rib abnormalities.