Obesity subjects individuals into metabolic and endocrine disorders. Thus obesity may increase the risk of vitamin D deficiency. This text aims at studying the prevalence of vitamin D deficiency and secondary hyperparathyroidism in obese children. In a non-randomized case control study on 52 obese children (body mass index (BMI)>95th percentile) aged 4 to 16 years undertaken at the outpatient endocrine clinic of the Children Hospital at Tabriz University between 2009–2011. This study was conducted to compare the prevalence of vitamin D deficiency and secondary hyperparathyroidism in obese children compared with 57 non obese (BMI< 85th percentile). 109 children including 52 (50.5%) boys and 57 (49.5%) girls were studied. Most of case (76.9%) and control (42.1%) groups suffered from degrees of vitamin D deficiency. There was meaningful statistical difference between two groups considering to vitamin D deficiency and parathyroid hormone (p = 0.001). A negative relations was found between iPTH and vit D level (p<0.001, r=–0.2), BMI and 25-OH vit D (p<0.001, r=–0.2). A positive relation was observed between parathyroid hormone and BMI (p=0.009, r=0.1). Obese children are at high risk at vitamin D deficiency and secondary hyperparathyroidism. BMI appears to be an important risk factor for vitamin D deficiency.