We report on a Japanese female with 45,X[40]/46,X, der(X)[60], primary amenorrhea, and tall stature. She was confirmed to have complete gonadal dysgenesis at 19 yr of age and was placed on hormone replacement therapy. Growth assessment revealed that she had a low normal height until her early teens, but continued to grow with a nearly constant height velocity in her late teens, attaining a final height of 172 cm (+ 2.9 SD), which surpassed her target height range. Fluorescence in situ hybridization analysis for 10 loci/regions on the X-chromosome together with the whole X-chromosome and the Xp-specific and Xq-specific paintings showed that the der(X) chromosome was associated with duplication of roughly distal half of Xp, including SHOX (short stature homeobox-containing gene), and deletion of most of Xq. Microsatellite analysis for eight loci at Xp22 and nine loci at Xq26-28 indicated that the normal X-chromosome was of maternal origin, and the der(X) chromosome was of paternal origin. The results, in conjunction with the adult height data in 47,XXX, 46,XX gonadal dysgenesis, 47,XXY, 46,XY gonadal dysgenesis, and 46,X, idic(Xq-), suggest that the tall stature of this female is caused by the combined effects of SHOX duplication on the der(X) chromosome and gonadal estrogen deficiency. Furthermore, the similarity in the growth pattern between this female and patients with estrogen resistance or aromatase deficiency implies that the association of an extra copy of SHOX with gonadal estrogen deficiency may represent the further clinical entity for tall stature resulting from continued growth in late teens or into adulthood.