The avian mutation, nanomelia, is an autosomal recessive embryonic lethal. Homozygous embryos show hypoplasia of the limbs and a parrot-like beak. Biochemical studies have associated this phenotype with the absence of the major cartilage-specific proteoglycan core protein. In a previous study, a DNA polymorphism was identified at the 3' end of the core protein gene by using denaturing gradient gel electrophoresis. This polymorphism is characterized by three electrophoretic variants (alleles), two of which are associated with the normal core protein gene and one of which segregates with the nanomelia mutation. This study documents that segregation of the latter electrophoretic variant can be used to substitute for progeny testing in the identification of carriers of the nanomelia mutation. Standard progeny phenotype tests were carried out in conjunction with genotype screening for the putative nanomelia-associated electrophoretic variant. We found the genotype data defining the nanomelia core protein gene locus to correlate with progeny phenotype test results.