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Klinefelter syndrome is most commonly associated with a 47,XXY karyotype, though rarer variants such as 48,XXXY, 48,XXYY, 49,XXXXY, and mosaic forms occur. The clinical spectrum includes intellectual disability, psychiatric disorders, endocrinopathies, and infertility, while epilepsy is rarely reported. The syndrome is also linked to an increased risk of malignancies, including breast cancer and mediastinal germ cell tumors. Multinodular and vacuolating neuronal tumors (MVNTs) are rare glioneuronal neoplasms.

We report a 9-year-old male with a 2-year history of epilepsy, in whom brain MRI revealed an MVNT in the left posterior temporal lobe. Chromosomal microarray analysis showed a 2.5 Mb duplication at Xp22.33, a 152.9 Mb duplication from Xp22.33 to Xq28, and a 280 kb deletion at 5q33.1. Karyotyping confirmed a 47,XXY karyotype, consistent with Klinefelter syndrome.

While MVNTs are typically sporadic or monogenic, this case raises the possibility of an association with Klinefelter syndrome. To our knowledge, this is the second reported case, contributing to the expanding clinical and genetic spectrum of Klinefelter syndrome-associated neurological findings.