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While Klinefelter Syndrome (KS) has a prevalence of 85–250 per 100,000 born males, patients are typically underdiagnosed due to a subtle phenotype emerging only late during puberty or adulthood. Rare cases of KS carry a mosaic phenotype 47-XXY/46-XY associated to mild phenotypic traits mostly compatible with a normal life including preserved fertility. From a genetic modeling perspective, the derivation of naturally isogenic iPSCs from mosaic patients allows the comparison of disease and healthy cells carrying a virtually identical genomic background.