Alternative pre-mRNA splicing generates multiple mRNA isoforms of different structures and functions from a single gene. While the prevalence of alternative splicing control is widely recognized, and the underlying regulatory mechanisms have long been studied, the physiological relevance and biological necessity for alternative splicing are only slowly being revealed. Significant inroads have been made in the brain, where alternative splicing regulation is particularly pervasive and conserved. We show alternative splicing plays an instructive role in axonogenesis and synaptogenesis. Our studies demonstrate important RNA binding proteins and their targets coordinate various aspects in establishing neuronal identity.