Mice homozygous for the autosomal recessive gene, cartilage matrix deficiency (cmd/cmd), are characterized by disproportionate dwarfism and cleft palate. The collagen and proteoglycan of fetal limb cartilage was examined by biochemical and immunofluorescent techniques. While a normal amount of type II collagen was found, the amount of proteoglycan was reduced as determined by chemical analysis and incorporation of labeled precursors. Analyses of labeled proteoglycans by glycerol density gradient centrifugation under dissociative conditions and by gel filtration showed that the major high molecular weight proteoglycan characteristic of cartilage was absent, but smaller proteoglycans were present in normal amounts. Antibodies directed against proteoglycan core protein failed to stain the cmd/cmd cartilage while antibodies to type II collagen stained the cartilage without hyaluronidase pretreatment. Addition of beta-D-xyloside, an exogenous substrate for chondroitin sulfate synthesis, and direct assay for beta-D-xylosyltransferase activity indicated that cmd/cmd cartilage cells contained normal levels of the enzymes required for chondroitin sulfate synthesis. The data suggest that cmd/cmd is defective in the synthesis of the cartilage proteoglycan core protein.