In this study, ligament fibroblasts were cultivated on micropatterned silicone substrates and subjected to cyclic stretching to simulate the in vivo biomechanical environment during ligament healing. Without stretching, ligament fibroblasts were aligned parallel to the microgrooves on the silicone substrate surface. However, we previously reported that uniaxial cyclic stretching induces alignment perpendicular to the stretching axis. With stretching on a microgrooved surface, cell proliferation and collagen production were greatly enhanced. The exact functions of the micropatterned surface and mechanical stimuli are unknown. Therefore, in gene expression microarray experiments, genes whose expression is inhibited by subculture from passage 0 (P0) to passage 8 (P8) and enhanced by micropatterning and stretching were sought out. The following six genes were selected: MGP, GADD45A, UNC5B, TGFB1, COL4A1, and COL4A2. The selected genes play fundamental roles in cell proliferation, differentiation, apoptosis, and structural maintenance. On the basis of the obtained gene expression profiles, we identified candidate genes that might be involved in responses to a micropatterned surface and mechanical stretching.