This paper reports the case of a 16-year-old woman with idiopathic short stature (ISS) who was detected to be haploinsufficient in only exon 1 of the short stature homeobox-containing (SHOX) gene by RQ-PCR and had two copies of the other six exons intact. The translation of the SHOX protein and of the SHOX promoter may be potentially affected if the deletion of exon 1 is extended further upstream. Further studies may help in determining the significance of partial exonic deletions of the SHOX gene in relation to ISS.