To describe the phenotype of a large group of children with congenital hypothyroidism (CH) and iodide organification defect (IOD), suspected based on normal thyroid position and abnormal perchlorate discharge test, as first step of a project evaluating correlations between phenotypes and genotypes. 71 children born in Paris between 1980 and 2006 were included. Two groups were defined according to perchlorate discharge: total IOD (TIOD) when the release was above 90% and partial IOD (PIOD) between 10 and 90%. Comparisons between groups were performed using SPSS 14.0 for Windows. The incidence of IOD over the 2003–2006 period was 1: 20,660. Of the 71 children, 61 had PIOD and 10 TIOD. Compared to PIOD, TIOD was characterized by greater clinical severity. A wide spectrum of clinical features was seen in the PIOD group. Evolution showed transient hypothyroidism in 10/61 patients with PIOD and 1/10 TIOD patients. Severe presentation in the majority of TIOD patients suggests dysfunction of a key iodide-organification enzyme. In contrast, the variety of clinical features in PIOD group suggests that diverse mechanisms may lead to PIOD, such as delayed or reduced activity of enzymes involved in hormonogenesis or defects in iodine storage and release.