Background In order to suggest an ideal source of adult stem cells for the treatment of nervous system diseases, MSCs from human adipose tissue and bone marrow were isolated and studied to explore the differences with regard to cell morphology, surface markers, neuronal differentiation capacity, especially the synapse structure formation and the secretion of neurotrophic factors. Methods The neuronal differentiation capacity of human mesenchymal stem cells from adipose tissue (hADSCs) and bone marrow (hBMSCs) was determined based on nissl body and synapse structure formation, and neural factor secretion function. hADSCs and hBMSCs were isolated and differentiated into neuron-like cells with rat brain-conditioned medium, a potentially rich source of neuronal differentiation promoting signals. Specific neuronal proteins and neural factors were detected by immunohistochemistry and enzyme-linked immunosorbent assay analysis, respectively. Results Flow cytometric analysis showed that both cell types had similar phenotypes. Cell growth curves showed that hADSCs proliferated more quickly than hBMSCs. Both kinds of cells were capable of osteogenic and adipogenic differentiation. The morphology of hADSCs and hBMSCs changed during neuronal differentiation and displayed neuron-like cell appearance after 14 days' differentiation. Both hADSCs and hBMSCs were able to differentiate into neuron-like cells based on their production of neuron specific proteins including beta-tubulin-III, neuron-specific enolase (NSE), nissl bodies, and their ability to secrete brain derived neurotrophic factor (BDNF) and nerve growth factor (NGF). Assessment of synaptop hysin and growth-associated protein-43 (GAP-43) suggested synapse structure formation in differentiated hADSCs and hBMSCs. Conclusions Our results demonstrate that hADSCs have neuronal differentiation potential similar to hBMSC, but with a higher proliferation capacity than hBMSC. Adipose tissue is abundant, easily available and would be a potential ideal source of adult stem cells for neural-related clinical research and application.