We present the immunohistochemical study of 11 cases of intracranial cysts: two extraventricular ependymal cysts, three colloid cysts of the third ventricle, four extraventricular choroidal cysts and two Rathke's cleft cysts. Antibodies against glial fibrillary acidic protein (GFAP), cytokeratins (AE1, CK5D, AE3), S-100 protein, epithelial membrane antigen (EMA), vimentin, neuron specific enolase (NSE), neurofilaments protein (NF) and prealbumin, were used. The epithelium of choroidal cysts, showed strong immunoreactivity for Prealbumin and cytokeratins, similar to the normal choroid plexus epithelium. The ependymal cysts showed epithelial immunoreactivity for GFAP and S-100, both glial markers expressed by the normal ependymal epithelium. On the contrary, the epithelial wall of colloid cysts and Rathke's cleft cyst, expressed epithelial markers (cytokeratins and EMA) but no neuroepithelial markers, with a immuno-phenotype similar to that of other cysts of endodermal nature. This finding supports the neuroepithelial origin for choroid and ependymal cysts, and an endodermal nature for colloid and Rathke's cleft cysts. We conclude that these immunohistochemical markers are useful in the differential diagnosis of intracranial cysts.