Engineering the osteochondral junction requires fabrication of a microenvironment that supports both osteogenesis and chondrogenesis. Multiphasic scaffold strategies utilizing a combination of soluble factors and extracellular matrix components are ideally suited for such applications. In this work, we evaluated the contribution of an osteogenic nanoparticulate mineralized glycosaminoglycan scaffold (MC-GAG) and a dually chondrogenic and osteogenic growth factor, BMP-9, in the differentiation of primary human mesenchymal stem cells (hMSCs). Although two dimensional cultures demonstrated alkaline phosphatase activity and mineralization of hMSCs induced by BMP-9, MC-GAG scaffolds did not demonstrate significant differences in collagen I expression, osteopontin expression, or mineralization. Instead, BMP-9 increased expression of collagen II, Sox9, aggrecan (ACAN), and cartilage oligomeric protein (COMP). However, the hypertrophic chondrocyte marker, collagen X, was not elevated with BMP-9 treatment. In addition, histologic analyses demonstrated that while BMP-9 did not increase mineralization, BMP-9 treatment resulted in an increase of sulfated glycosaminoglycans. Thus, the combination of BMP-9 and MC-GAG stimulated chondrocytic and osteogenic differentiation of hMSCs.