Chordoid glioma has been recently described as a slow-growing neoplasm with chordoid appearance, occurring exclusively in the regions of the third ventricle and hypothalamus of middle-aged women. We experienced a case of a 48-year-old woman with a suprasellar tumor composed of chordoid glioma and Rathke's cleft cyst, which was confirmed by histopathological, immunohistochemical and electron microscopic examinations. Histologically, chordoid glioma comprised the major part of the tumor, and the prominent Rathke's cleft cysts were distributed focally in the same tumor tissue without any transitions. Chordoid glioma was immunoreactive for glial fibrillary acidic protein, S-100 protein and vimentin, and focally positive for epithelial membrane antigen and CD34, while cytokeratin highlighted epithelial cells lining Rathke's cleft cysts. Ultrastructural examination of the chordoid glioma revealed short cytoplasmic processes, intermediate filaments, intercellular junctions of zonular adherens type, basal lamina, secretory granules and pinocytic vesicles. The ultrastructural observations of the current case are similar to those of the subcommisural organ, although cell body zonation or microvilli were not evident. The coexistence of chordoid glioma and Rathke's cleft cyst has not been reported previously and may represent a collision tumor.