Abstract A novel mathematical model to simulate mesenchymal stem cells differentiation into specialized cells is proposed. The model is based upon material balances for extracellular matrix compounds, growth factors and nutrients coupled with a mass-structured population balance describing cell growth, proliferation and differentiation. The proposed model is written in a general form and it may be used to simulate a generic cell differentiation pathway occurring in vivo or during in vitro cultivation when specific growth factors are used. Literature experimental data concerning the differentiation of mesenchymal stem cells into chondrocytes in terms of total DNA and glycosaminoglycan content are successfully compared with model results, thus demonstrating the validity of the proposed model as well as its predictive capability. A further test of the model capability is performed for the case of in vivo fracture healing during which mesenchymal stem cells differentiate into chondrocytes and osteoblasts. Considerations about the extension of the proposed model to different pathologies beside fracture healing are reported. Finally, sensitivity analysis of model parameters is also performed in order to clarify what mechanisms most strongly influence differentiation and the distribution of cell types.