Aim: In the present study, the effect of different dose of boric acid (B) on viability, morphology and some biochemical characteristic of rat bone marrow mesenchymal stem cells (MSCs) were investigated.Material and Methods: MSCs after 3rd passage was treated with 0.6, 3 and 6 nano, micro and milligram/ml of B for 12, 24 and 36hrs. The viability was estimated using 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assay and the dose of 6 Nano, micro and milligram/ml and 36hrs was chosen to continue the investigation. The cell proliferation base on colony forming assay and population doubling number (PDN) was studied; also the morphology of the cells was investigated using florescent dye. The concentration of total calcium and the activity of the enzymes Alanine aminotransferase, aspartate aminotransferase, lactate dehydrogenase and alkaline phosphatase was estimated. Data was analyzed using ANOVA.Results: Treatment of the cells with all the doses caused the viability to decrease significantly after 36hrs. Morphology of the nuclei and cytoplasm as well as number and diameter of the colonies showed significant reduction due to the treatments. Whereas treatment with 6 mg/ml caused significant decrease of the PDN after 1, 3 and 6 days. In addition significant decrease of the activity of Alanine aminotransferase, aspartate aminotransferase and lactate dehydrogenase were observed in response to treatment with all the doses. Treatment with 6ng and mg/ml caused significant increase in the alkaline phosphatase activity and total calcium concentration, whereas 6mg/ml left no effect on total calcium level and alkaline phosphatase activity.Conclusion: Treatment of MSCs with mg dosage of B showed toxicity, but regarding some factors we observed positive results with respect to nano and microgram dosage, therefore more research is recommended.