Key points: Between 2006 and 2013, 3,207 children were diagnosed with fetal alcohol spectrum disorders (FASD) during their hospital stay in the neonatal period, representing 0.48 cases per 1,000 births, including 0.07 cases of fetal alcohol syndrome (FAS) per 1,000 births. At the regional level, the proportion of children diagnosed with FASD was highest in Réunion (1.22‰), Upper Normandy (1.02‰), Champagne-Ardenne (0.90‰), and Nord-Pas-de-Calais (0.90‰). Between the periods 2006–2009 and 2010–2013, there was a significant decrease in the number of children diagnosed with FAS but an increase in the number of other fetal alcohol spectrum disorders (aFASD). These results likely underestimate the prevalence of FASD, particularly due to the difficulty in identifying children with such disorders. These results are difficult to compare with previous French studies because the methodologies differ: here, the coding stage in hospital registries likely adds an additional level of underestimation, which may vary by region.