Female genital mutilation (FGM) concerns an estimated half a million women in Europe. The studies based in countries where migrant women have settled highlight the need for more accurate information on FGM health consequences, in a European health care context. Excision and Handicap (ExH) is a multi-centric survey based on case–control methodology and conducted in France to assess the long-term consequences of FGM, sampling both FGM and non-FGM adult women. The interviews were conducted in 74 mother-and-child health centres and hospital departments providing gynaecological and family planning services in five French regions. The two groups were compared on health indicators (self-perceived health, illnesses, symptoms) and functioning indicators (daily, sexual and reproductive life) for cases (n = 678) and controls (n = 1706). Multivariate logistic models highlighted FGM-related health problems. Among women living in France, FGM was significantly associated with poor health indicators: gynaecological and urinary infections (OR = 2.0), sleep disorders (OR = 1.4), intense pain (OR = 1.5), difficulties in daily life (OR = 1.5) and in sexual life (OR = 1.7) or tearing during childbirth (OR = 1.6). Our results suggest that, even in a favourable healthcare context, FGM exposes women to long-term health problems, including in areas neglected in previous research. They confirm the need to establish recommendations to help physicians understand these women's needs.