A higher frequency of extra-thyroidal congenital malformations (ETCM) has been reported in children with congenital hypothyroidism (CH) compared with the general population. The most commonly reported one, congenital cardiac malformation (CCM), is reported to be in the range of 2-29% which is much higher than in normal population with a prevalence of 0.8%. Our aim is to investigate the frequency and type of additional ETCM in children with congenital hypothyroidism due to thyroid dysgenesis (TD) born between 1991 and 2013. We included 41 children with confirmed primary CH due to TD and excluded patients with Down syndrome. Age at diagnosis ranged from 4 days to 4 years. The aetiology of TD was determined with thyroid ultrasound and scintigraphy. Malformations were identified by physical examination, echocardiography abdominal/renal ultrasound and X-ray. Twenty-seven of the 41 patients had ectopic thyroid (66%), 12 had thyroid agenesis (29%) and 2 had hemiagenesis (5%). A high level of ETCM (48%, n:20) was observed. Nine patients had more than one system malformation. The most frequent malformation was CCM (22% n:9), consisting of atrial septal defect (15%, n:6), mitral insufficiency (5%, n:2), pulmonary stenosis (2%, n:1). There was a high prevalence of ETCM in patients with thyroid dysgenesis especially cardiac. Patients at least should be screened for cardiac anomalies.