Background: Growth retardation following malnutrition is prevalent among patients with congenital heart diseases (CHDs). This study was designed to evaluate failure to thrive (FTT) and delay in bone age in children with CHDs who were referred to our hospital and subsequently to determine their relation with cyanosis and the pulmonary artery pressure. Methods: We enrolled 120 consecutive patients who were referred to Rajaie Cardiovascular, Medical, and Research Center for cardiac catheterization or surgical correction. Growth parameters, comprising height (cm), weight (kg), and head circumference (cm), were measured by an experienced nurse. Bone age was evaluated by taking an anteroposterior wrist X-ray and reported by a radiologist, who was not aware of the exact cardiac diagnosis. The pulmonary artery pressure was measured during cardiac catheterization or surgical correction. Results: Bone growth retardation, FTT, short stature, and microcephaly were seen in 46.6%, 43.7%, 29.4%, and 5.1% of the patients, correspondingly. There was a significant relationship between the presence of cyanosis and delayed bone age, particularly when O2 saturation was less than 75% (P < 0.0001). The presence of pulmonary hypertension was significantly related to a higher rate of bone growth retardation (P < 0.0001). FTT and delayed bone age were significantly different between the cyanotic patients and the children with pulmonary hypertension and the acyanotic patients and those without pulmonary hypertension (P < 0.05). Conclusions: According to our results, delayed bone age and growth retardation are common findings in children with CHDs. The presence of cyanosis and/or pulmonary hypertension may further deteriorate these conditions and should be promptly managed. (Iranian Heart Journal 2017; 18(3):35-41)