To describe pontine axonal anomalies across diverse brain malformations. Institutional review board–approved review of magnetic resonance imaging (MRI) and genetic testing of 31 children with brain malformations and abnormal pons by diffusion tensor imaging. Anomalous dorsal pontocerebellar tracts were seen in mid-hindbrain anomalies and in diffuse malformations of cortical development including lissencephaly, gyral disorganization with dysplastic basal ganglia, presumed congenital fibrosis of extraocular muscles type 3, and in callosal agenesis without malformations of cortical development. Heterotopic and hypoplastic corticospinal tracts were seen in callosal agenesis and in focal malformations of cortical development. There were no patterns by chromosomal microarray analysis in the non-lissencephalic brains. In lissencephaly, there was no relationship between severity, deletion size, or appearance of the pontocerebellar tract. Pontine axonal anomalies may relate to defects in precerebellar neuronal migration, chemotactic signaling of the pontine neurons, and/or corticospinal tract pathfinding and collateral branching not detectable with routine genetic testing.