Short stature with different alterations in the skeletal appearance usually results from juvenile hypothyroidism. The present case-control study was conducted to assess the effect of thyroid hormone deficiency on the height of young people and the prevalence of short stature in juvenile hypothyroidism. The research was conducted at the Al-Waffa Diabetic Centre between May and September 2022. The study group included 90 children with short stature, while the control group included 58 children. The statistical analysis was conducted using Minitab version 20. The results revealed that a low serum level of triiodothyronine (T3) was present in 2.2% of participants, while a low serum level of thyroxin (T4) was present in 36.7%. All subjects had elevated serum thyroid stimulating hormone (TSH). Female children had increased rates of short stature. Juvenile hypothyroidism results in various skeletal manifestations, including reduced height. Low serum thyroxin coupled with high serum thyroid stimulating hormone are common findings in juvenile hypothyroidism.