Bilateral periventricular nodular heterotopia (BPNH) is a neuronal migration disorder that is characterized by subependymal nodules of gray matter. Recently, a causative gene for BPNH, filamin 1, has been identified, and possible roles of the translated protein in cell migration and blood vessel development have been proposed. We report here the histopathological features of an autopsy case of BPNH with widespread glomeruloid microvascular anomaly and dysplastic cytoarchitecture in the cerebral cortex, in whom we found a novel exon 11 (Val528Met) filamin 1 mutation. Within the periventricular nodules, well-differentiated pyramidal neurons were randomly oriented. A small proportion of neurons were immunolabeled with antibodies raised against calbindin D-28k, parvalbumin, or calretinin. We used a carbocyanine dye (DiI) tracing technique to investigate the extent of fiber projections within and outside the nodules. The labeled fibers formed bundles that extended into the surrounding white matter. Connections between adjacent nodules were evident. Connections between the nodules and the cerebral cortex were also seen, with a small number of labeled fibers reaching the cortex. In the cerebral cortex, small closely packed vessels ran in a parallel fashion throughout all of the layers. Immunohistochemically, the inner rim of individual vessel lumina was labeled by an antibody against factor VIII, and the vessel walls were labeled by antibodies against actin and laminin. Astrocyte processes, labeled with an antibody to glial fibrillary acidic protein, invaded these vascular channels. Ultrastructurally, a network of basal lamina-like materials lined with endothelial cells was evident. The cytoarchitecture of the cerebral cortex was disturbed, in that the columnar neuronal arrangement was distorted around the malformed vessels. This case appears to represent an example of BPNH manifesting widespread developmental anomalies within the blood vessels and the cortical cytoarchitecture in the cerebrum.