Spinal Muscular Atrophy is a devastating motor neuron disease affecting primarily children. SMA is caused by mutations and deletion in the SMN1 gene, leading to low SMN levels in affected in individuals. Despite a clear involvement of other tissue types, motor neurons appear to be the most vulnerable cell type to reduced SMN levels. Indeed the predominant symptom in this disease is progressive paralysis, due to denervation of skeletal muscle and loss of motor neurons. Over the past few years, we have been focused on using mouse models of SMA to investigate the cellular consequences of reduced Smn levels on the motor unit. It is now well established a loss of neuromuscular junctions is an early and significant event in SMA. We have also shown that this loss of neuromuscular junctions (NMJ) appears to be coupled to a reduction in their anatomical plasticity and capacity to remodel, and this reduction in plasticity appears associated with an increase in their vulnerability. Furthermore, the loss of neuromuscular junctions appears to vary between different muscles. In both mouse models and patients with SMA, there appear to be extreme weakness in some muscles groups, while other remain relatively unaffected. We believe that understanding the differences between these differentially vulnerable motor units will give insight into the reasons why motor neurons are selectively vulnerable in SMA, and help us develop therapeutic strategies for how to protect them.