Abstract SHOX gene mutations or haploinsufficiency cause a wide range of phenotypes such as L eri W eill dyschondrosteosis ( LWD ), T urner syndrome, and disproportionate short stature ( DSS ). However, this gene has also been found to be mutated in cases of idiopathic short stature ( ISS ) with a 3–15% frequency. In this study, the multiplex ligation‐dependent probe amplification ( MLPA ) technique was employed to determine the frequency of SHOX gene mutations and their conserved noncoding elements ( CNE ) in C olombian patients with ISS . Patients were referred from different centers around the county. From a sample of 62 patients, 8.1% deletions and insertions in the intragenic regions and in the CNE were found. This result is similar to others published in other countries. Moreover, an isolated case of CNE 9 duplication and a new intron 6b deletion in another patient, associated with ISS , are described. This is one of the first studies of a L atin A merican population in which deletions/duplications of the SHOX gene and its CNE are examined in patients with ISS .