Morquio A, a lysosomal storage disease due to a deficiency in N-acetylgalactosamine-6-sulfate sulfatase (GALNS), results in the glycosaminoglycan accumulation of chondroitin-6-sulfate (C6S) and keratan sulfate (KS) causing chondrodysplasia. Using aggregate culture technique with murine mesenchymal stromal cells (MSCs) obtained from adipose tissue in wild-type and Morquio A mice we evaluated if GALNS deficiency would result in differences of gene expression during the in vitro chondrogenesis process. Sox9 and Runx2 expressed during the earlier stages of chondrogenesis were higher in wild-type compared to Morquio A MSCs during the first week of culture. Genes associated with the hypertrophic phenotype of chondrocytes, alkaline phosphatase and collagen type 10, were higher in Morquio A aggregates compared to wild-type during the second and third week of induction. In conclusion, we have identified differences in gene expression levels between wild-type and Morquio A mice MSCs associated with in vitro chondrogenesis. To further understand glycosaminoglycan catabolic activities during chondrogenesis we evaluated three lysosomal enzymes using aggregate culture technique with human adipose tissue derived MSCs. During chondrogenic induction enzyme activity for GALNS decreased significantly during the three weeks of culture. Subsequent degradation of C6S and KS is carried out by beta-galactosidase, and enzyme activity had a similar pattern compared to GALNS. On the other hand, β-glucuronidase catabolizing dermatan sulfate, heparan sulfate, C4S and C6S had a more homogenous pattern of activity during the three weeks of culture. These results suggest enzyme activity during aggregate culture could be implicated in the in vitro chondrogenesis process.