Background aims. The purpose of this study was to investigate the neuroprotective effects of bone marrow bone marrow derived and adipose tissue derived mesenchymal stromal cells (MSCs) that welt intravitreally transplanted in an experimental ocular hypertension (OHT) model. Methods. An OHT rat model was generated by means of intracameral injection of hyaluronic acid into the anterior chamber. MSCs labeled with green fluorescence protein were transplanted intravitreally 1 week after OHT induction. At the end of the second and fourth weeks, retinal ganglion cells were visualized with the use of a flat-mount retina:method and were evaluated by means of immunofluorescence staining against green fluorescence protein, vimentin, CD 105, and cytokines (interleukin [IL]-1Ra, prostaglandin E2 receptor, IL-6, transforming growth factor-beta 1, interferon-gamma and tumor necrosis factor-alpha). Results. The retinal ganglion cell numbers per area were significantly improved in stem cell treated OHT groups compared with that in the non-treated OHT group (P < 0.05). The results of immunohistochemical analyses indicated that a limited number of stem cells had integrated into the ganglion cell layer and the inner nuclear layer. The number of cells expressing proinflammatory cytokines (interferon-gamma and tumor necrosis factor-alpha) decreased in the MSC-transferred group compared with that in the OHT group after 4 weeks (P < 0.01). On the other hand, IL-1Ra and prostaglandin E2 receptor expressions were increased in the rat bone marrow derived MSC group but were more significant in the rat adipose tissue derived MSC group (P < 0.01). Conclusions. After intravitreal transplantation, MSCs showed a neuroprotective effect in the rat OHT model. Therefore, MSCs promise an alternative therapy approach for functional recovery in the treatment of glaucoma.