Screening for congenital hypothyroidism (CH) at birth has been conducted in France since 1978, under the auspices of the French Association for the Screening and Prevention of Childhood Disabilities (AFDPHE). A preliminary analysis of screening data had shown an increase in the annual incidence rates of CH with intact thyroid gland (ITG) between 1984 and 2010. A study of additional data available since 2002 was conducted to analyze the characteristics of children with CH diagnosed at birth, to investigate whether these characteristics contributed to the increase in incidence rates between 2002 and 2012, and to describe regional disparities in incidence rates. A total of 2,722 cases of CH were diagnosed between 2002 and 2012. Among them, 1,021 (37.5%) had CH with GEP, and 1,701 (62.5%) had dysgenesis (athyreosis, ectopic thyroid). Newborns with CH and dysgenesis were predominantly female (71%), born at term with a birth weight (BW) similar to that of the general newborn population, whereas newborns with CH and PGE had a balanced sex ratio and were more frequently low birth weight (14.1% with BW < 2,500 g or 5.5% with BW < -2 standard deviations (SD)) and preterm (14.2%) than the general newborn population in the National Perinatal Surveys. Incidence rates were 33.0 cases per 100,000 for overall CH; 11.8 cases per 100,000 for CH with GEP; and 19.7 cases per 100,000 for CH with dysgenesis. From 2002 to 2012, an average annual increase in incidence of 7.7% (p<0.0001) was observed among HC with GEP, whereas rates among HC with dysgenesis remained stable (p=0.4). Regional disparities in the incidence of HC with GEP were observed, with higher rates in Picardy and Franche-Comté. The factors explaining regional disparities and the increase in the incidence of HC with GEP in France during the 2002–2012 period warrant further investigation through additional studies.