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A 12 year old girl referred for chromosome analysis because of short stature was found to have karyotype mos 45,X/46,X,+mar. The marker chromosome was observed in 58% of her blood lymphocytes. It was a small, pale staining, spherical fragment with GTL banding and showed faint differentiation along its length with CBG banding. DNA analysis using Y specific probes showed the absence of the testicular determining region and the presence of some short arm and centromeric Y chromosomal material. In situ hybridisation confirmed that the Y chromosomal material was associated with the marker chromosome. At laparotomy the patient was found to have streak gonads. Gonadectomy was subsequently performed and histological examination showed dysgenetic gonads with a dysgerminoma arising from a gonadoblastoma in the left gonad. This case shows that even very small Y derived marker chromosomes with pericentric material can predispose the phenotypic female to gonadal neoplasia.