We describe a pediatric case with a complex phenotype resulting from the coexistence of two distinct genetic diagnoses—cerebrotendinous xanthomatosis (CTX), a rare autosomal recessive lipid storage disorder caused by biallelic mutations in the CYP27A1 gene and Klinefelter syndrome a common sex chromosome aneuploidy occurring in approximately 1 in 600 males, characterized by hypogonadism, gynecomastia, pubertal delay, infertility, micrognathia, and neurodevelopmental challenges—and an additional incidental finding with clinical relevance. Here, CYP27A1 is linked to Klinefelter syndrome.