Objectives: The use of growth hormone (GH) in idiopathic short stature (ISS) has been a subject of debate for the past two decades. We sought to assess the effect of GH on final height (FH) in patients with ISS in our region, which has a high consanguinity rate, and compare it to the effect observed in GH deficient (GHD) patients. Methods: We conducted a retrospective chart review from 1 January 2005 to 31 December 2013 for patients with ISS or GHD from the local United Arab Emirates population who received GH treatment and were followed-up regularly in our clinic. The change in height Z-score at 12 months and FH were assessed within each group and between the two groups. Results: Twenty-one patients with ISS and 29 patients with GHD were studied. There was a significant change in height Z-score at 12 months and FH in both groups (p < 0.001). The improvement in the ISS group was comparable to the response seen in GHD patients at 12 months (0.5±0.3 standard deviation score (SDS), and 0.5±0.4 SDS, respectively; p = 0.540). The effect on FH was better in ISS group than the GHD group of all etiologies (1.3±0.6 SDS vs. 0.9±0.7 SDS, respectively; p = 0.050), there was no difference between the ISS and the subgroup of idiopathic GHD (1.3±0.5 SDS and 1.2±0.8 SDS, respectively). Conclusions: In our local population, GH has a positive effect on the short-term growth and FH of children with ISS to the same extent that has been observed in children with idiopathic GH deficiency.