Objectives: Females' genital mutilation still remains to be a serious problem for large proportion of women in most sub-Saharan Africa countries including Ethiopia. Therefore, the aim of this study is to determine the prevalence of female genital mutilations and its associations with the birth complications among women attending delivery service in Nigist Eleni Mohammed General Hospital, Hossana, Ethiopia from 02 May 2015 to 29 June 2015. Methods: Hospital-based cross-sectional study design was used to collect data from a sample of 395 women on prevalence of female genital mutilation and its association with birth complications. Data was coded, cleaned and entered into a computer data base by using EPI Info version 3.5.3, and then analysed by using SPSS version 20.0. Descriptive summary values such as frequency and percentage was used to describe the study variables. A bivariate and multivariate logistic regression analysis with a confidence level of 95% was performed. Variables with p-value <0.05 in the bivariate analysis were transferred into multivariate logistic regression analysis to control the effect of confounders. Results: Out of 395 women, 364 (92.2%) of them practiced female genital mutilation and most of the operation was done by a non-medical practitioner, 265 (67.1%). The prevalence of birth complications among the study participants was 245 (62.0%). The likely hood of the occurrence of birth complications was 2.45 and 2.99 times more likely common among Kembeta [AOR=2.45 (95% CI;1.30, 4.61)] and Silite [AOR=2.99 (95% CI, 1.16, 7.67)], respectively when compared to women from Hadiya ethnic group. Conclusion: In general, female genital mutilation is highly prevalent among the study participants and most of the operation was done by a non-medical practitioner. The prevalence of birth complications is also high among the study participants. Therefore, a multi-sectoral approaches should be considered to reduce the problem and to promote safe delivery.