To assess bone mineral density (BMD) of children with short stature using quantitative ultrasound (QUS) and compare it to children with normal height. Methods: We conducted a descriptive, cross-sectional controlled study between May 2018 and February 2019 at various pediatric clinics in Jeddah, Saudi Arabia. In total, 219 children were included: 100 had short stature, and 119 were of normal height. Data were collected from one-on-one interviews, and BMD was measured using quantitative ultrasound. Results: Children with short stature had significantly lower BMD z-scores than children with normal height (pless than 0.05). The use of vitamin D supplements was related to higher BMD z-scores in children with short stature (p less than 0.05). A significant association was found between higher BMD z-scores, and both age (p=0.05) and height (p=0.02). Through a further division of children with short stature into those with and those without growth hormone deficiencies, we show that growth hormone deficiency was positively associated with lower BMD z-scores; however, the p-value was 0.06. Conclusions: Compared with children of normal height, those with short stature had lower BMD. Height, vitamin D supplementation, and age were all significantly correlated with higher BMD, while growth hormone deficiency was correlated with lower BMD.