Abstract Routine cell stains disclose abnormal, usually single, nests of ectopic neurons in neocortical layer I of New Zealand Black (NZB) and BXSB autoimmune mice. We have suggested that these anomalies represent only the most visible part of more widespread cortical disorganization. In an attempt to determine the true magnitude of cellular and fiber disruption associated with the presence of ectopias, we stained cortical sections containing ectopias in layer I from NZB and BXSB mice with an antibody directed against the 68 kDa subunit of neurofilament protein. The neurofilament-stained sections revealed substantial disruption of the cortical layers underlying the ectopic neurons. This resulted primarily from the existence of dense, radially oriented fiber bundles spanning the thickness of the cortex underlying the ectopias. In some instances these fiber bundles could be seen to join the corpus callosum. Even in a small ectopia, where standard stains show no associated cortical dysplasia, dense neurofilament staining was present in layers II and III. It was concluded that the brains of autoimmune mice have severe developmental cortical disorganization, which could account for the behavioral differences displayed by these animals.