Background Chordoid neoplasms refer to tumors appearing to have histological features of embryonic notochord, which is characterized by cords and lobules of neoplastic cells arranged within myxoid matrix. Because of radiological and histological similarities with myxoid matrix and overlapping immunohistochemical profile, chordoma, chordoid meningioma, chordoid glioma, and rare extraskeletal myxoid chondrosarcoma enter in the radiological and histological differential diagnosis at the site of skull base. However, there is always a great challenge for histopathologists to make an accurate diagnosis when encountering a chordoid neoplasm within or near the central nervous system. The aim of this study is to investigate and summarize the radiological, histological features and immunohistochemical profiles of chordoid neoplasms in skull base, and to find a judicious panel of immunostains to unquestionably help in diagnostically challenging cases. Methods A total of 23 cases of chordoid neoplasms in skull base, including 10 chordomas, 5 chordoid meningiomas, 3 chordoid gliomas and 5 extraskeletal myxoid chondrosarcomas, were collected from the First Affiliated Hospital, Sun Yat-sen University and Guangdong Tongjiang Hospital. MRI examination was performed on the patients before surgical treatment. Microscopical examination and immunohistochemical staining study using vimentin (Vim), pan-cytokeratin (PCK), epithelial membrane antigen (EMA), S-100 protein (S-100), glial fibrillary acidic protein (GFAP), D2-40, Galectin-3, CD3, CD20, Ki-67 were performed on the samples of cases. The clinicopathological data of the patients was also analyzed retrospectively. Results Most of chordomas were localized in the clivus with heterogeneous hyperintensity on T2WI scanning. The breakage of clivus was observed in most cases. Histologically, the tumor cells of chordoma exhibited bland nuclear features and some contained abundant vacuolated cytoplasm (the so-called physaliferous cells) within myxoid matrix. Areas of cartilage presented in individual cases. The tumor cells of chordoma were diffusely immuno-positive for PCK and EMA. Chordoid meningioma is characterized by a homogeneous contrast-enhancing mass with dural tail sign. The epithelioid cells were arranged in cords and clusters within a myxoid matrix, which was highly reminiscent of chordoma. The ratio of myxoid component and conventional meningioma was different in tumors. EMA was detectable in all chordoid meningiomas, and 4/5 cases were positive for D2-40. That was a finding which was helpful in distinguishing chordoid meningioma from chordoma. Chordoid gliomas were localized in the third ventricle with homogeneous enhancement on MRI examination. The tumors were composed of clusters and cords of epithelioid tumor cells within a variably mucinous stroma containing lymphoplasmacytic infiltratation. The most distinctive immunohistochemical feature of chordoid gliomas is their strong diffuse reactivity for GFAP. EMA and PCK positive expression can also be seen focally in individual cases. Although extraskeletal myxoid chondrosarcomas share the similar radiological and histological appearance with chordoma, all chondrosarcomas in the present study are completely negative for epithelial markers except for immuno-positivity of S-100 focally. In addition, Galectin-3 can be detected in most of chordoid neoplasms in skull base. Conclusion The specific localization and MRI features of tumors are useful diagnostic clues for the differential diagnosis of chordoid neoplasms in skull base. However, combining with histological features, a panel of selected immunostains, including PCK, EMA, GFAP, S-100 and D2-40, is helpful in making an accurate diagnosis for those diagnostically challenging cases which usually appear to have atypical radiological features or in an unusual site. Ki-67 index and Galectin⁃3 are not recommended to use as diagnostic markers for chordoid neoplasms of skull base because of their less neoplastic specificity.