Several groups of investigators have reported an increased incidence of congenital anomalies in patients with congenital hypothyroidism. Furthermore, in patients with congenital hypothyroidism and mutations in genes known to be involved in thyroid development, specific extra-thyroidal abnormalities have been observed. The goal of the present study was to gain insight in the types and patterns of morphological characteristics depending on the type of congenital hypothyroidism of thyroidal origin (CH-T). In 242 Dutch CH-T patients with a thyroid agenesis, a dystopic thyroid rudiment or a eutopic thyroid gland, we performed a careful physical examination of the body surface directed to visually detectable morphological abnormalities; results were compared to a group of 1,007 Dutch control subjects. The percentage of patients with one or more major abnormalities in the total CH-T cohort (33.1%) and in patients with CH-T dystopic thyroid (37.2%) was significantly higher than in the control population (21.8%; P < 0.001). Especially in the CH-T dystopic thyroid group specific major malformations (bilateral ear pits; oligodontia) were found more frequently. Also, the percentage of patients in the total CH-T group with one or more minor anomalies (96.3%) was significantly higher than in the control group (82.5%). The careful grouping of patients according to their CH-T etiology and the types and patterns in morphological findings may be helpful in the search for novel genes involved in thyroid development.