Topographic cues have been recognized crucial on the modulation of cell behavior, and subsequent important for the design of implants, cell-based biomedical devices and tissue-engineered products. Grooved topography direct cells to align anisotropically on the substrates, resulting in an obvious morphological difference compared with the flat and the other topographies. This study aimed at investigating the effects of grooved topography on the differentiation of mesenchymal stem cells (MSCs) into osteoblasts, adipocytes and myoblasts. A series of submicron-grooved polystyrene substrates with equal groove-to-ridge ratio but different width and depth (width/depth (nm): 450/100, 450/350, 900/100, and 900/550) were fabricated based on electron beam lithography and soft lithography techniques. Primary rat MSCs (rMSCs) were cultured on these substrates without induction for differentiation for 6 days, and then subjected to induction for osteogenesis, adipogenesis and myogenesis. While the alignment of rMSCs strongly complied with the direction of the grooves and increased with groove depths, cell attachment on day 1 (~1.5 × 10(4)/cm(2)) and cell proliferation after 6 days of culture (~5 × 10(4)/cm(2)) were not significantly affected by substrate types. Osteogenesis, indicated by alkaline phosphatase activities and calcium deposit, was not significantly modulated by the grooved substrates, compared with the flat control, suggesting that cell alignment may not determine osteoinduction of rMSCs. On the other hand, adipogenesis, indicated by lipid production, was significantly enhanced by the grooved substrates compared with the flat surface (P < 0.001). On the other hand, myogenesis, indicated by desmin and MHC staining, was enhanced by the grooves in a time- and groove size-dependent manner compared with the flat control. The results suggested that grooved topography has an in-depth potential for modulating the commitment of the stem cell lineages, which could benefit the development of advanced biomaterials for biomedical applications.