Hypoparathyroidism is the most common complication following thyroidectomy. There are few population-based reports on the rate of hypoparathyroidism in children. The incidence of medical treatment of permanent hypoparathyroidism in children is reported using a national registry. The study population included patients below 18 years of age undergoing total thyroidectomy reported to the Scandinavian Quality Registry for Thyroid, Parathyroid and Adrenal Surgery 2004-2014. Patients with previous thyroid or parathyroid surgery or treatment with vitamin D before surgery were excluded from analysis. Permanent postoperative hypoparathyroidism was defined as treatment with vitamin D for more than 6 months after thyroidectomy. Risk factors for permanent hypoparathyroidism were calculated with uni- and multivariable logistic regression. Using data from the Swedish Inpatient Registry, rates of readmissions and annual number of days in hospital after total thyroidectomy were compared between patients with and without permanent hypoparathyroidism. Some 274 children (215 girls and 59 boys) underwent total thyroidectomy. The median age was 14 (range 0-17) years. Indications for surgery were Graves' disease (214, 78.1%), other benign disease (27, 9.9%) and thyroid cancer (33, 12%). Median follow-up was 4.8 years. Twenty (7.3%) children developed permanent hypoparathyroidism. No statistically significant risk factors for permanent hypoparathyroidism were identified. Rates of readmission and annual number of days in hospital after discharge were similar in patients with and without permanent hypoparathyroidism. The rate of permanent hypoparathyroidism following total thyroidectomy in children was high and is a cause of concern.