Aim To investigate extracellular matrix (ECM) characteristics of cortical bone and articular cartilage of patients with Morquio syndrome A, a lysosomal storage disease caused by a deficiency of N-acetylgalactosamine-6-sulfate sulfatase. Patients and methods Cartilage, bone, and fibroblasts from 2 unrelated patients with Morquio syndrome were used. Histological analysis on bone and cartilage was carried out by means of light and electron microscopy. Lysyl hydroxylation and cross-linking of collagen present in bone, cartilage, and fibroblast cultures was determined by reverse-phase high performance liquid chromatography. Results No histological or biochemical differences were seen in cortical bone; furthermore, no differences were seen in the amount and modification of collagen deposited by fibroblasts. Articular cartilage showed major differences: collagen fibrils show a wider range of fibril diameter, the fibrils are in mean thicker, the lysyl hydroxylation level of the triple helix is strongly decreased, the total amount of pyridinolines is in the lower ranges, and the ratio hydroxylysylpyridinoline to lysylpyridinoline is decreased. Changes were also observed with respect to the arrangement of proteoglycans in the extracellular matrix surrounding the chondrocytes. Conclusion The collagen of bone and the collagen deposited by fibroblasts is normal, whereas the ECM of cartilage in Morquio syndrome A patients is affected. Thus, deficiency in N-acetylgalactosamine-6-sulfate sulfatase has an impact on the phenotypic properties of chondrocytes, resulting in the formation of cartilage that is more prone to degeneration, being an explanation for the occurrence of osteoarthritis in Morquio syndrome A patients at early age.