Our aim was to investigate effects of chronic hypoxia on endocrine function in pediatric patients with cyanotic congenital heart disease (CHD). Thirty patients with cyanotic CHD (16 boys, 14 girls), and 35 control subjects (22 boys, 13 girls) were enrolled. Age means of patients and controls were 4.37±4.51 and 4.28±4.96 years, respectively. Standard deviation scores (SDS) of height and weight were significantly lower among patients compared to controls. Mean fasting glucose levels were 75±15 mg/dL and 83±12 mg/dL among patients and controls, respectively (p=0.033). Insulin-like growth factor (IGF) 1 and its SDS were significantly lower among patients (p=0.010). There was no significant difference in ACTH and cortisol levels between groups. ACTH levels were very low in six patients. Oxygen saturation level was positively correlated with ACTH (p=0.041, r=0.439) and negatively correlated with HOMA-IR (p=0.046, r=-0.420) and insulin (p=0.017, r=-0.494). There was no difference in insulin resistance between groups. Chronic hypoxia has negative impact on growth by reducing IGF-1 along with the nutritional deficiency in children with cyanotic CHD. ACTHadrenal axis is also affected. While cyanotic CHD has decreased serum glucose level, it had no effect on insulin level and insulin resistance. Negative correlations between oxygen saturation, and HOMA-IR, fasting insulin levels, have suggested that these patients should be monitorized for insulin resistance.