Antibodies to the amyloid precursor proteins (APP) have become routine markers for detecting traumatically induced axonal injury (AI) in animals and man. Unfortunately, the techniques used to visualize these proteins are not compatible with routine electron microscopic (EM) analysis. In the current communication, we describe a method for the ultrastructural visualization of antibodies to APP and, using this method, we identify a previously unrecognized population of traumatically injured axons. Rats were subjected to an impact acceleration traumatic brain injury and allowed to survive 30 min to 3h postinjury. The animals were then perfused, their brains sectioned on a vibratome and the sections prepared for immunocytochemistry using a computer-controlled microwave capable of temperature regulation. The use of temperature-controlled microwave energy unmasked APP antigenic epitopes without sacrificing ultrastructural detail. The APP antibody was found in two distinct populations of reactive axons that differed in size, morphology, location, and temporal progression. Comparable to previous descriptions, one population showed traumatically related reactive changes that led to swelling and disconnection. The other population, however, revealed unanticipated changes reflected in nodal and paranodal swelling of small continuous fibers that showed no evidence of disconnection during the time periods assessed. These studies provide new insight into the complexity of the pathobiology of AI, while describing a novel approach for enhancing APP immunoreactivity at the EM level.