Objective: The current study was aimed to compare the quality of neuronal differentiation and reduction in apoptosis that occurred in two-dimensional (2D) and three-dimensional (3D) fibrin scaffold culture conditions. PC12 and embryonic stem cells are two commonly utilized cell lines for the study of neuronal regeneration. Materials and Methods: These cells were induced to neuronally differentiate by adding NGF and retinoic acid respectively. Total neurite length and expression of neuronal markers (MAP-2 and β3-tubulin) was assessed by morphometry and immunocytochemistry. Also, TUNEL assay was used to detect apoptosis. Results: Upon exposure to a differentiation media in the 3D fibrin gel, PC12 and embryonic stem cells stopped dividing, had increased adhesion to the substratum, extended neurite processes and expressed neuronal markers. The same results, however, were not observed with the 2D culture. Also, the apoptosis index performed by TUNEL demonstrated a reduction in the degree of apoptosis in the 3D culture compared to 2D culture (p =0.001). 3D fibrin scaffolds support growth and neuronal differentiation of PC12 and embryonic stem cells. In addition, the 3D culture enhanced cellular resistance to apoptosis when compared to the 2D culture. Conclusion: It appears as if a 3D culture system may offer a better technique for future neuronal tissue engineering investigations.