In previous investigations, we have shown para-nonylphenol (p-NP) caused significant reduction of proliferation and differentiation of rat bone marrow mesenchymal stem cells (MSCs) in vitro. In this study, we first treat the rats with p-NP, then carried out the biochemical and morphological studies on MSCs. Proliferation property of cells was evaluated with the help of MTT assay, trypan blue, population doubling number, and colony forming assay. Differentiation property was evaluated with quantitative alizarin red assay, measurement of alkaline phosphatase (ALP) activity as well as intracellular calcium content. In addition; morphological study, TUNEL test, activated caspase assay, and comet assay were performed to evaluate the mechanism of the cell death. The results showed significant reduction in the colony-forming-ability and population-doubling-number of extracted cells when compared to control ones. In addition, it was revealed that the p-NP treatment of rats caused significant reduction in nuclear diameter, cytoplasm shrinkage, and induction of caspase-dependent-apoptosis. Also there was significant reduction in ALP activity, intracellular calcium content, and intracellular matrix following osteogenic differentiation. As MSCs are the cellular back up for bone remodeling and repair, we suggest more investigations to be conducted regarding the correlation between the increasing number of patients suffering from osteoporosis and p-NP toxicity. Also, we strongly recommend WHO and local health organization to prevent industries of using p-NP in formulation of industrial products which may cause changes in proliferation and differentiation properties of stem cells.