We describe a male with a variant Klinefelter syndrome (KS), and trisomy Xq resulting from an isochromosome Xq [47,Xi(Xq)Y]. He had many characteristics of classical KS: bilateral atrophic testes and microcalcifications, normal masculinization, azoospermia, hypergonadotropic hypogonadism, elevated FSH and LH, normal intelligence and normal androgenization, but his stature was not increased. Ultrasonographic evaluation also revealed parenchymal alterations secondary to previous epididymo-orchitis. After initial evaluation the patient underwent incisional biopsy of testes which showed tubular hyalinisation, Leydig cell hyperplasia and Certoli cell syndrome. The i(Xq) was found in all cells analyzed. These findings indicate that extra copies of the long arm of X have phenotypic expression, even though activated only in early development. In conclusion, review of literature on 20 adult patients supports the view that the presence of an isochromosome Xq in KS has a favorable prognosis in terms of normal mental development and normal stature.