We recently reported that some, but not all, axotomized propriospinal commissural interneurons (PCI) of the adult mammal can regenerate through spinal midsagittal transection injury sites (Fenrich and Rose [2009] J Neurosci 29:12145-12158). In this model, regenerating axons grow through a lesion site surrounded by a dense deposition of chondroitin sulfate proteoglycans (CSPG), which are typically inhibitory to regenerating axons. However, the mechanisms that lead some regenerating axons to grow through spinal cord injury (SCI) sites while others remain trapped in the CSPG zones or retract to their soma remain unknown. As a first step toward elucidating these mechanisms, here we show that the ability of PCI axons to regenerate across a SCI site depends on the branching patterns of their distal terminals. Using 3D reconstruction techniques through multiple serial sections and immunohistochemical analyses, we found that at 7 days postinjury a majority of PCI axons terminated in CSPG zones ipsilateral of the spinal midline. Conversely, at 9 days postinjury some PCI axons had regenerated across the midline, but others terminated outside the CSPG zones near their soma. Furthermore, we show that the most successful regenerators were those with the most extensive branching patterns, whereas those that terminated outside the CSPG zones had terminal regions indistinguishable from dystrophic terminals. Our results demonstrate that the morphological characteristics of regenerating axons play an important role in their ability to regenerate across SCI sites, and that the branching patterns of some regenerating axons are more extensive and have a far greater complexity than previously reported.