Spinal muscular atrophy (SMA) is one of the most common genetic disorders that cause infant mortality. SMA is caused by loss of the Survival of Motor Neuron (SMN) protein, resulting in motor neuron degeneration in the spinal cord. Although SMN protein plays diverse roles in cells and is expressed in all cells, it is unclear why a deficiency in SMN only causes motoneuron degeneration. Since patient samples are rarely available, most knowledge in SMA is gained from animal model studies. While these studies have provided important information concerning the cause and mechanism of SMA, they are limited by complicated genetic manipulation. Results from different models are also not always consistent. These problems can be resolved if SMA patient’s motoneurons become readily available. The progress in the generation of stem cell lines from differentiated adult cells, termed induced pluripotent stem cells (iPSCs), provides an opportunity to establish human cell-based models for neurodegenerative diseases like SMA. We have previously established several SMA iPSC lines from a type 1 patient and showed specific deficits in motoneurons derived from these iPSCs. The availability of these iPSCs provides an opportunity to explore the mechanisms of selective motoneuron degeneration in SMA. We used motoneurons derived from SMA iPSCs to study potential defects in the formation of neuromuscular junctions. We also demonstrated a regulatory gene product affected by SMN deficiency. Several potential downstream targets of the regulatory gene product involved in neuron migration and synaptic transmission were identified. The roles of these genes in selective motoneuron degeneration observed in SMA are currently under study. One technical obstacle of using iPSC-derived motoneurons to study SMA in a dish is that motoneurons generally constitute only a fraction of the resulting cell population. The lack of capacity to isolate motoneurons hampers our study of SMA pathogenesis and the identification of potential downstream targets of SMN. We have employed a new approach, termed gene editing, to mark differentiated motoneurons with a fluorescence protein to facilitate their isolation by cell sorting. A proof-of-principle experiment was carried out and demonstrated the feasibility of this strategy. We are currently applying this strategy to mark motoneurons derived from SMA iPSCs.