The effect of hypothyroidism on kidney size has not been studied in children. The aim of this study was to examine the role of congenital hypothyroidism and levothyroxine (L-thyroxine) treatment on renal growth. Forty children with congenital hypothyroidism and 37 healthy controls were prospectively included. The mean age of patients was 8.2 +/- 4.7 years. Patients had lower height and weight standard deviation scores compared with controls. The mean L-thyroxine initial age and treatment duration were 37.0 and 60.5 months, respectively. In 62.5% of patients, L-thyroxine was initiated after 6 months of age, and 60.0% of patients had severe hypothyroidism. Patients had lower kidney length and total kidney volume compared with controls (P<0.05). No significant differences were found in kidney volume/body weight and kidney volume/body height ratios between patients and controls (P>0.05). Multiple regression analysis showed significant relationship between relative kidney volume and average free thyroxine level (P<0.05). No significant differences in kidney sizes were found between patients who had L-thyroxine initiated before and after 6 months of age or between mild/moderate and severe hypothyroidism at diagnosis (P>0.05). In conclusion, normal renal growth can be accomplished with L-thyroxine replacement despite considerable delay in treatment initiation and/or severe hypothyroidism.