Semaphorins were initially characterized according to their role in repulsive axon guidance but are now recognized as crucial regulators of morphogenesis and homeostasis over a wide range of organ systems. The pleiotropic nature of semaphorin signaling and its implication in human disease has triggered an enormous interest in the receptor and intracellular signaling mechanisms that direct the cell-type-specific and diverse biological effects of semaphorins. Recent breakthroughs in our understanding of semaphorin signaling link integrin and semaphorin signaling pathways, identify novel ligand–receptor interactions and provide insight into the cellular and molecular bases of bifunctional and reverse signaling events. These discoveries could lead to therapeutic advances in axonal regeneration, cancer and other diseases.