Deletions or mutations in survival of motor neuron 1 (SMN1) cause motor neuron loss and spinal muscular atrophy (SMA), a neuromuscular disorder, with the most severe type manifesting in utero. Whether SMA is a disease of defects in neurodevelopment and/or neuromaintenance remains unclear. We performed an analysis of Smn gene and protein expression during murine embryogenesis. Furthermore, we examined Smn(-/-);SMN2 mice, a model of very severe SMA, for developmental, morphological, and molecular abnormalities. We demonstrate that Smn transcript levels are regulated in a tissue- and developmental stage-specific manner and that the Smn protein expression pattern generally followed that of the Smn mRNA. Cell death and pathological foci were observed in E10.5 Smn-depleted embryos, and this increased in the telencephalon at E14.5. Furthermore, we show an altered morphology of cranial nerves as well as truncated lumbar spinal nerves in a subset of E10.5 Smn(-/-);SMN2 embryos. Finally, we compared the splicing of a subset of genes shown recently to be aberrantly spliced in phenotypic-stage SMA mice. Changes in alternative splicing of the Slc38a5 and Uspl1 genes were detectable in prephenotypic-stage embryos and neonates but became more pronounced with the severity of the phenotype. By comparison, Hif3a alternative splicing was affected only at the end stage of disease. This result suggests that alterations in mRNA splicing in SMA occur, in part, as a result of disease progression. Overall, we conclude that Smn depletion affects developmental processes, which ultimately may also contribute to SMA pathogenesis.