Mice with targeted disruptions in retinoic acid receptor genes have been generated to assess the role of nuclear receptors as transducers of the retinoid signal during vertebrate development. Mice with mutations that disrupt all isoforms of the RAR alpha, RAR beta and RAR gamma genes as well as for the individual RAR alpha 1, RAR beta 2 and RAR gamma 2 have been described. By breeding the RAR alpha 1 and RAR beta strains together we have generated double mutants which have striking phenotypes not discernible in mice homozygous for the individual mutations. Mice lacking both RAR alpha 1 and RAR beta died shortly after birth because of hypoxia, although individual RAR alpha 1 and RAR beta mutants were phenotypically normal. As previously observed in RAR compound mutants, histological examination of 18.5 dpc fetuses of RAR alpha 1 -/-beta-/- double mutants revealed a number of congenital malformations which in many respects were similar to those observed in fetuses of vitamin A-deficient mothers. The regions of congenital defects in RAR alpha 1 -/-beta-/- double mutants included the eye, the skull, the respiratory tract, the heart, the aortic arch-derived great vessels, and urogenital system. The penetrance of malformations in RAR alpha 1 -/-beta-/- mutants was greater than that in the reported RAR alpha 1 -/-beta 2-/- double mutants. Moreover, RAR alpha 1 -/-beta-/- mutants exhibited hypoplastic lungs and ossified fusion between basioccipital and exoccipital bones that were not reported in the RAR alpha 1 -/-beta2-/- animals, and displayed ectopic thymus and an unique defect in testis suggesting specific roles for RAR beta 1, 3 and/or 4 isoforms in these structures. The RAR alpha 1 single mutant animals as well as RAR alpha 1-/- beta-/- double mutant mice were susceptible to the teratogenic effects of RA, demonstrating that RAR alpha 1 and RAR beta isoforms singly or in combination do not play a major role in RA-induced craniofacial malformation and limb deformities.