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Introduction Basal encephalocele is rare in adults. Congenital and acquired cases have been reported with regard to the developmental mechanism, and the pathology has not been elucidated in detail. Case presentation We encountered an adult with basal encephalocele strongly suggesting congenital development because of the presence of minor anomalies: strabismus and ocular hypertelorism. The disease manifested as persistent spontaneous cerebrospinal fluid rhinorrhea and repeated meningitis in a 66-year-old Japanese man. On computed tomography, brain tissue protruded through a part of the ethmoid bone of his right anterior skull base, and it was diagnosed as transethmoidal-type basal encephalocele. Regarding his facial form, the distance between his bilateral eyeballs was large compared to his facial width, and his canthal index (defined as inner to outer inter canthal ratio × 100) was calculated as 38.5, based on which it was judged as ocular hypertelorism. In addition, his right eyeball showed strabismus. A right frontotemporal craniotomy was performed for spontaneous cerebrospinal fluid rhinorrhea, and the defective dura mater region was patched with temporal fascia. Conclusions Mild minor anomalies that require no treatment are overlooked in adults, but the presence of several anomalies increases the possibility of congenital disease. Therefore, it may be necessary to examine minor anomalies in cases of adult basal encephalocele when considering the possibility that the disease may be congenital. [ABSTRACT FROM AUTHOR]