We report on the case of a 34-year-old patient with the Klinefelter syndrome and an unusual cytogenetic finding of a deletion involving the short arm of the X chromosome. This was confirmed with fluorescent in situ hybridization (FISH) using an X chromosome-specific whole chromosome painting probe. The patient presented with infertility. The only abnormal physical findings were atrophic testes with azoospermia and elevated levels of follicle-stimulating hormone and luteinizing hormone. This case represents a relatively mild manifestation of the Klinefelter syndrome. Previous reported cases were often associated with more severe phenotypes such as variable degrees of mental retardation and facial dysmorphism, hypothesized as due to the failure of X inactivation. The X inactivation center, located on Xq13, is presumably intact in our patient, who had a deletion involving only the short arm. The mild phenotype observed in our patient was found to be consistent with the conventional and molecular cytogenetic findings.