The SH-SY5Y cell line is commonly used for the assessment of neurotoxicity in drug discovery. These neuroblastoma-derived cells can be differentiated into neurons using many methods. The present study has compared 24 of these differentiation methods on SH-SY5Y cells. After morphologic selection of the three most differentiating media (retinoic acid in 10% fetal bovine serum (FBS), staurosporine in 1% FBS medium, and cyclic adenosine monophosphate (cAMP) in B21-supplemented neurobasal medium), cells were analyzed for pan-neuronal and specific neuronal protein expression by fluorescent automated imaging. The response of SH-SY5Y to a set of compounds of known toxicity was examined in these culture conditions performed in 2D, and also in a 3D hyaluronic acid-based hydroscaffold™ which mimics the extracellular matrix. The extent of neuronal markers expression and the sensitivity to neurotoxic compounds varied according to the differentiation medium. The cAMP B21-supplemented neurobasal medium led to the higher neuronal differentiation, and the higher sensitivity to neurotoxic compounds. The culture in 3D modified the neurotoxic response, through a lower sensitivity of cells compared to the 2D culture. The in vitro differentiation environment influences the neurotoxic response of SH-SY5Y cells and thus should be considered carefully in research as well as in drug discovery.