Previous studies in the rodent brain have characterised the cell types present in the subependymal layer, however the general organisation and cellular morphology of the adult human subependymal layer has not been demonstrated previously. In this study, we have demonstrated that the normal human brain subependymal layer contains three morphologically distinct types of cells, A, B and C type cells. The type A cells resembling migrating neuroblasts were located in the superficial part of the subependymal layer, type B cells resembling glial cells were evenly distributed throughout the subependymal layer and caudate nucleus, and type C cells that resembled progenitor cells were located in the deeper regions of the subependymal layer close to the caudate nucleus. We also examined the subependymal layer in the Huntington's disease brain to determine whether neurodegenerative pathology of the caudate nucleus (adjacent to the subependymal layer) altered the cellular composition of the subependymal layer. In the Huntington's disease subependymal layer there was a significant increase in the thickness of the subependymal layer compared with the normal subependymal layer (p < 0.01) and there was a 2.8-fold increase in the number of cells present in the Huntington's disease subependymal layer compared with the normal subependymal layer but the density of cells remained unchanged. As the grade of Huntington's disease increased, so did the overall number of cells in the subependymal layer. An increase in the number of type B cells was responsible for most of the increase demonstrated, however there was also an increase in the numbers of type A and C cells. To further characterise the human normal and Huntington's disease subependymal layer we used immunohistochemistry and antibodies against a range of projection neuron markers, interneuron markers, glial cell markers and GABAA receptor subunits. The results demonstrated the presence of increased numbers of neuropeptide Y positive cells in the Huntington's disease subependymal layer compared with the normal subependymal layer, suggesting that neuropeptide Y neurons may play a role in progenitor cell proliferation. Also there was an increased level of the developmentally active GABAA receptor subunit gamma 2 that indicates that the adult subependymal layer still retains the ability to proliferate. Taken together our results give a detailed description of the adult human subependymal layer and also demonstrate the plasticity of the human subependymal layer in response to Huntington's disease.