In order strengthen activities against female genital mutilation (FGM), this study aimed to assess the prevalence of childbirth complications due to FGM in the province of Gourma, Burkina Faso. The cross-sectional study was both descriptive and analytical; it was conducted between June 15 and August 15, 2007. The sampling was comprehensive, incorporating all of the women who gave birth in the four maternity wards in Fada Ngourma, the provincial capital. The survey included an interview, clinical examination and document analysis of archives and records. The 354 respondents were younger than 25 years-old in 58% of the cases, and 78% of all women participating were illiterate. FGM was Type I, II or III for 28%, 28% and 3% for them respectively. Obstructed labor occurred in 29% of the cases, and a caesarean section was preformed in 7% of the cases. Of all the normal vaginal deliveries, 24% required episiotomies, 18% experienced obstetric Hemorrhaging, 20% had uterine retroversion and 3% needed blood transfusions. Among the newborns, 5% were resuscitated and 4% were stillbirths. The existence of FGM has statistically increased the proportion of dystocia (OR = 11.5), cesarean section (OR = 17.6), episiotomy (OR = 64), perineal tears (OR = 10, 2), postpartum hemorrhage (OR = 13.0), retroverted uterus (OR = 14.7), blood transfusions (OR = 8.0) and stillbirths (OR = 10.2). Women with FGM Type 2 and 3 were more prone to dystocia and obstructed labor (OR = 5.7) and cesarean delivery (OR = 5.2) than those with FGM Type 1. FGM constitutes an important risk factor for complications during childbirth. It should be eradicated for good health of the mother, newborn and child in Burkina Faso.