A mesenchymal stem cell (MSC)-seeded collagen gel under static or dynamic tension is a well-established model to study the potential of MSCs in regenerating a tendon- or ligament-like tissue. Using this model, upregulation of fibrillar collagen mRNA expression and protein production has been demonstrated in response to cyclic tensile mechanical stimulation. However, the mechanisms driving MSC tenogenesis (differentiation into tendon or ligament fibroblasts) have not been elucidated. This study investigated the mechanisms of tenogenesis of human bone marrow-derived MSCs in a dynamic, three-dimensional (3D) tissue-engineering model by investigating the effects of cyclic stretching on matrix production and gene expression of candidate tendon and ligament markers. The 3D MSC tenogenesis culture system upregulated scleraxis, but cyclic stretching was required to maintain expression of this putative tendon marker over time. Enhanced tendinous neo-tissue development demonstrated with extracellular matrix staining was largely due to changes in matrix deposition and remodeling activity under dynamic loading conditions, as evidenced by differential regulation of matrix metalloproteinases at a transcriptional level with minimal changes in collagen mRNA levels. Regulation of Wnt gene expression with cyclic stimulation suggested a similar role for Wnt4 versus Wnt5a in tenogenesis as in cartilage development. This first report of the potential involvement of matrix remodeling and Wnt signaling during tenogenesis of human MSCs in a dynamic, 3D tissue-engineering model provides insights into the mechanisms of tenogenesis in a mechanoactive environment and supports the therapeutic potential of adult stem cells.