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Background Female genital mutilation (FGM) is commonly practiced in sub-Saharan Africa and results in adverse pregnancy outcomes among affected women. This paper assessed the prevalence and effects of FGM on pregnancy outcomes in a rural Ghanaian setting. Methods We analyzed 9306 delivery records between 2003 and 2013 from the Navrongo War Memorial Hospital. Multivariable logistic regression analyses were used to determine the effects of FGM on pregnancy outcomes such as stillbirth, birth weight, postpartum haemorrhage, caesarean and instrumental delivery. We also assessed differences in the duration of stay in the hospital by FGM status. Results A greater proportion of mothers with FGM (24.7%) were older than 35 years compared with those without FGM (7.6%). FGM declined progressively from 28.4% in 2003 to 0.6% in 2013. Mothers with FGM were nearly twice as likely to have caesarean delivery (adjusted odds ratios = 1.85 with 95%CI [1.72, 1.99]) and stillbirths (1.60 [1.21, 2.11]) compared with those without. Similarly, they had a 4-fold increased risk of post-partum haemorrhage (4.69 [3.74, 5.88]) and more than 2-fold risk lacerations/episiotomy (2.57 [1.86, 3.21]) during delivery. Average duration of stay in the hospital was higher for mothers with FGM from 2003 to 2007. Conclusions Despite significant decline in prevalence of FGM, adverse obstetric outcomes are still high among affected women. Increased public health education of circumcised women on these outcomes would help improve institutional deliveries and heighten awareness and prompt clinical decisions among healthcare workers. Further scale-up of community level interventions are required to completely eliminate FGM. [ABSTRACT FROM AUTHOR]