The osteochondrodysplasia rat, inherited by a single autosomal recessive lethal gene ocd, shows a typical dwarfing syndrome with systemic subcutaneous edema. The skeletal system is most severely affected. The affected newborn also demonstrates abnormal kidney position and respiratory system anomalies and central nervous malfunction. Previous light microscopic observations show that the chondrocytes are expanded and destroyed, and the amounts of extracellular matrix (ECM) and glycosaminoglycans (GAGs) are decreased. The present studies describe ultrastructural appearances, and measurement and electrophoretic analysis of the major components of the cartilaginous GAGs. Decrease in amounts of ECM and swollen chondrocytes with the expanded organelles were reconfirmed in the ocd/ocd by electron microscopic observation. The large expanded vesicles contained unevenly distributed granular materials and large ruthenium red (RR) granules. The RR granules in the ECM were small and most parts of the collagen fibers did not associate with the granule in the ocd/ocd, while the RR granules attached to all the collagen fibers in the phenotypically normal (+/?). There were large collagen bundles in the region where the chondrocytes were committed to self-destruction. The biochemical analysis of the cartilage showed that noncollagenous proteins were increased and the GAGs were decreased in amount in the ocd/ocd, although the hydroxyproline content was comparable to that of the +/?. The hyaluronic acid was close to the limit of detection by electrophoresis of the cartilaginous GAGs in the ocd/ocd. These results suggest that the ocd gene affects GAG metabolism. The decrease in amounts of GAGs, especially hyaluronic acid, may be responsible for the anomalies of the cartilage in the ocd/ocd.