Objective On rare occasions, yolk sac tumor may arise from extragonadal sites. Orbit is an unusual location for the primary development of this tumor. The presence of intracranial yolk sac tumor on biopsy always makes the diagnosis challenge for pathologists. Herein we report a case of intracranial primary yolk sac tumor in left orbital apex. The clinicopathology of this tumor and its differential diagnosis are discussed. Methods The clinical manifestation of a patient with primary yolk sac tumor occurring in left orbital apex was presented retrospectively. Resected orbital mass was routinely paraffin⁃embedded and stained with hematoxylin and eosin. Dako Envision immunohistochemical staining system was used to detect the tumor antigen expressions, including alpha ⁃fetoprotein (AFP), cytokeratin, placental alkaline phosphatase (PLAP), CD30, CD34, CD45, CD99, CD117, synaptophysin (Syn) and chromogranin A (CgA). Results A 2⁃year⁃old boy presented with 3⁃month history of ptosis of eyelid and exophthalmos on left eye. Magnetic resonance imaging (MRI) scan revealed a lesion occupied the left orbital apex with infiltration of surrounding normal structure, including left posterior ethmoid sinus, the wall of left maxillary sinus and sphenoid. However, there was no evidence of tumor infiltrating in brain parenchyma. Craniotomy was performed and the tumor was removed by en bloc resection. Grossly, the biopsy specimen received in small pieces was 1.20 cm × 1.00 cm × 1.00 cm when aggregated. No fibrous capsule, necrosis, haemorrhage and gross calcification were found in the tissue fragments. Histological examination revealed that the tumor was arranged in a reticular pattern. The cells were relatively large with a clear cytoplasm and vesicular nuclei. Scattered mitotic figures were noted. Schiller ⁃ Duval bodies and periodic acid ⁃ Schiff (PAS) positive (eosinophilic bodies) were evident in the tumor tissue. Immunohistochemical staining showed that the tumor cells were diffusely positive for cytokeratin (AE1/AE3) and focal positive for AFP, CD99 and CD117, but negative for PLAP, CD30, S ⁃ 100, CD45 and CD34. There was no evidence of mixture of other germ cell tumor component in this tumor by serial sections. Based on clinical presentation and histological findings, a final histological diagnosis of pure primary orbital yolk sac tumor, WHO grade Ⅳ, was made according to the criteria of WHO classification. The patient has not received chemotherapy and attended follow⁃up for 3 months, without any neurological deficit or signs of recurrence. Conclusion Despite the lower incidence, intracranial yolk sac tumors usually develop in the midline at the pineal or suprasellar regions occurring in children with distinctive histological features and immunohistochemical phenotypes. In general, intracranial yolk sac tumors are known to entail poor prognosis even after multidisciplinary treatment of operation, radiotherapy, and chemotherapy. It is noted that intracranial yolk sac tumor should be differentiated histologically from other types of germ cell tumors and mixed germ cell tumor. DOI:10.3969/j.issn.1672⁃6731.2012.01.019