Semaphorins constitute a family of signaling molecules with functions in axon pathfinding and neuronal migration. Neuropilins 1 and 2 have been identified as the ligand-binding component of semaphorin receptors. Both ligands and receptors are expressed in embryonic and adult organs in complementary and sometimes redundant patterns. In the present work, we compared the brain expression patterns of the class III semaphorins 3A, 3C, and 3F and neuropilins 1 and 2 between mouse and chick embryos at early developmental stages. Our studies revealed that expression of semaphorins is restricted in some cases to neuromeric transverse domains, to specific neuromeric boundaries, and to specific neuronal populations. Moreover, our studies also revealed coexpression of neuropilins and one or more semaphorins in some of the different expression sites. Comparison of the expression patterns between mouse and chick embryos showed large similarities, but important differences were also detected.