The effects of disodium ethane-1-hydroxy-1,1-diphosphonate (EHDP) and disodium dichloromethylene diphosphonate (Cl2MDP) on glycosaminoglycan synthesis and macromolecular organization of proteoglycans have been examined in normal adult canine cartilage. One to 500 micron of either compound produced reversible inhibition of glycosaminoglycan synthesis to about 70% of control levels, whereas lower concentrations had no effect. Based on Sephadex G-200 chromatography, the average hydrodynamic size of glycosaminoglycans in diphosphonate-treated cartilage was similar to that of those in control cartilage. In most cases proteoglycan aggregates from diphosphonate-treated cartilage were smaller in hydrodynamic size than those from control cartilage, as judged by Sepharose 2B elution profiles. The size of purified proteoglycan subunits, obtained after dissociation of the aggregates with 4 M guanidinium chloride or after incubation of the aggregates with hyaluronic acid beta1 leads to 3 hydrolase, was not affected by the diphosphonates. Furthermore, proteoglycans from diphosphonate-treated cartilage did not interact in vitro with hyaluronic acid, suggesting that diminished proteoglycan aggregation may have resulted from an abnormality in the hyaluronate-binding region of the proteoglycan core protein.