Purpose To assess the incidence of congenital hypothyroidism (CH) and acquired hypothyroidism (AH) between 2014 and 2019 in continental France. Methods New cases of CH and AH were identified using the French National Health Data System (Système Nationale des Données de Santé, SNDS). Temporal trends were studied using linear regression models. Spatial distributions were studied using Moran's global index (I) and the statistical method and local indicators of spatial association. Results The incidence of permanent CH in females increased by 8.9% per year (2014: 36.9 [31.1-43.7] per 100,000 birth-years vs. 2019: 51 [43.9-59.3] per 100,000 birth-years, p < 0.01). The incidence of AH decreased between 2014 and 2019 for both females (2014: 535.7 [533.2-538.2] per 100,000 person-years vs 2019: 335.5 [333.6-337.4] per 100,000 person-years, p < 0.01) and males (2014: 197.5 [195.9-199] per 100,000 person-years vs 2019: 141.7 [140.4-142.9] per 100,000 person-years, p<0.01). The incidence of hypothyroidism was high in the Nord-Pas-De-Calais and Lorraine regions (CH and AH). Conclusions The incidence of permanent CH in females has increased over time. AH incidence decreased. It seems necessary to investigate environmental factors in the disparity of incidence distribution.