The effects of Pongamia pinnata on stem cells have rarely been tested. This study aimed to evaluate the effects of the extract of Pongamia pinnata on the morphology and proliferation potential of the human gingival stem cells. Stem cells obtained from gingiva were cultured in a growth medium in the presence of Pongamia pinnata methanolic extract (PPT) at concentrations ranging from 0.001% to 1%. Evaluation of cell morphology and cellular viability were done at d’s 1, 3, 5 and 7. Immunofluorescent assays for collagen I and Runx2 were performed on d’s 1, 3, 5 and 7. Stem cells in the control group showed fibroblast-like morphology and the morphology of stem cells in the presence of PPT did not produce any noticeable changes. Low dose of PPT produced an increase in cell proliferation by 5 to 10%. However, higher dose of PPT of 1% group produced a significant decrease in cell proliferation. Noticeable increase of collagen I expression with noted with application of PPT, especially at 0.1%. Based on these findings, it was concluded that PPT could produce beneficial effects on mesenchymal stem cells with enhanced collagen I expression.