The formation of precise stereotypic connections in sensory systems is critical for defining accurate internal representations of the external world; however, the molecular mechanisms underlying the formation of sensory maps are poorly understood. Here, we examine the roles of two structurally unrelated repulsive guidance cues, semaphorin 3F (Sema3F) and Slit-1, in olfactory sensory axon fasciculation, targeting, and segregation. Using sema3F-/- mice, we show that Sema3F is critical for vomeronasal sensory neuron axonal fasciculation and for segregation of these sensory afferents from the main olfactory system; however, Sema3F plays only a minor role in targeting of apical vomeronasal neuron axons to the anterior accessory olfactory bulb (AOB). In addition, we show that Sema3F is required for lamina-specific targeting of olfactory sensory axons within the main olfactory system. In contrast to Sema3F, Slit-1 is dispensable for fasciculation of basal vomeronasal neuron axons but is critical for targeting these axons to the posterior AOB. These results reveal discrete and complementary roles for secreted semaphorins and slits in axonal targeting, fasciculation, and segregation of olfactory sensory neuron projections.