Neuronal networks in the spinal cord termed central pattern generators (CPGs) are responsible for the generation of rhythmic movements, such as walking. The axon guidance molecule EphA4 has been suggested to play a role in the configuration of spinal CPG networks in mammals. In EphA4 knockout (EphA4-KO) mice, the normal alternating walking pattern is replaced by a rabbit-like hopping gait, which can be reproduced when locomotor-like activity is induced in the isolated spinal cord. This hopping phenotype has been explained by an abnormal midline crossing of ipsilateral axons. Here, we investigated the nature of this overcrossing in heterozygous EphA4 (EphA4lacZ/+) mice that showed normal alternating gait and homozygous EphA4 (EphA4lacZ/lacZ) mice with hopping gait. Localized lesions showed that the hopping phenotype is maintained by fibers crossing in the ventral commissure. Using transgenic mouse lines in which glutamatergic, GABAergic and glycinergic neurons are intrinsically labeled, we showed a significant increase in the number of crossing excitatory β-galactosidase-positive neurons and a decrease in the number of inhibitory neurons crossing the midline in EphA4lacZ/lacZ mice compared with EphA4lacZ/+ mice. These results show that the hopping phenotype is the result of a change in the balance between excitatory and inhibitory signals across the midline and that EphA4-positive neurons play an essential role in the mammalian CPG.