Abstract Purpose Recent studies have shown an increased incidence of congenital hypothyroidism over the past 2 or 3 decades. The etiology of this change is unknown, but it has been related by several authors to lowering of cutoffs. We sought to determine whether the incidence of congenital hypothyroidism (CH) in France has changed. Methods We analyzed data from the nationwide neonatal screening program for CH during the period 1982–2012. We included all children having thyroid-stimulating hormone values above the threshold and for whom diagnosis of CH confirmed by the pediatrician. We estimated multicentric temporal trends in the annual incidence rates adjusted for screening methods for thyroid dysgenesis and eutopic gland. Results We found 6622 cases of CH (28.0 per 100,000 newborns); 1895 had a eutopic gland, and 4727 had thyroid dysgenesis. The incidence of eutopic glands showed a significant annual average increase of (5.1%; 95% confidence interval: 4.3–5.9) regardless of the screening method or screening center. This increase was confirmed in severe cases (thyroid-stimulating hormone ≥50: 2.1%; 95% confidence interval, 1.4–2.9). The incidence of dysgenesis remained constant. Conclusions The incidence of eutopic glands increased in France, not only in mild forms but also in severe cases.