The selection of a good quality scaffold is an essential strategy for tissue engineering. Ideally, the scaffold should be a functional and structural biomimetic of the native extracellular matrix and support multiple tissue morphogenesis. However, investigators have previously shown that three-dimensional nanofibrous scaffolds are capable of influencing cellular behavior. In this study, we experimented with a three-dimensional nanofibrous scaffold fabricated from aligned-poly L-lactic acid (PLLA) for its ability to support neurogenic and hinder dopaminergic differentiation of conjunctiva mesenchymal stem cells (CJMSCs) in vitro. In this work, CJMSCs were seeded onto nanofibrous scaffolds, and were induced to differentiate along neurogenic lineages by culturing in specific differentiation media. Scanning electron microscopy imaging, RT-PCR and immunocytochemistry were used to analyze cultivated CJMSCs on scaffold and their expression of neurogenic-specific markers. We found a lack of expression of dopaminergic genes in CJMSCs seeded on align PLLA scaffold, while neurocyte-cell markers including Nestin, NSE, MAP-2 and beta-Tubulin III were expressed in these cells. On the basis of these experimental results, we conclude that the nanofibrous PLLA scaffold reported herein could be used as a potential cell carrier in neural tissue engineering and that these scaffolds could be useful for the partial inhibition of the dopaminergic differentiation of CJMSCs.