Abstract Background Because infections with Schistosoma Haematobium usually peak in childhood, the majority of studies on schistosomiasis have focused on school-aged children. This study aimed to assess the epidemiological and clinical aspects of urogenital schistosomiasis in women in Burkina Faso, West Africa. Methods A cross-sectional study was conducted in a mesoendemic region (Kombissiri) and a hyperendemic region (Dori) for schistosomiasis in Burkina Faso. A total of 287 females aged 5 to 50 years were included in the study. S. haematobium infection was assessed using the urine filtration method and dipsticks were used for the detection of hematuria. Interviews were conducted to identify clinical aspects and risk factors related to urogenital schistosomiasis. Results The overall prevalence of S. haematobium infection in Dori was 21.3 %, where as Kombissiri was less affected with a prevalence of 4.6 %. The most affected age group was the 10- to 14-year-olds (41.2 %), followed by the 15- to 19-year-olds (26.3 %). Risk factors significantly associated with schistosomiasis (P <0.05) were place of residence, age, contact with open water in the past year, and distance of home to open water. The percentage of participants who had contact with open water was significantly higher among the women living in Dori compared to Kombissiri. Females over 15 years of age showed a significant higher rate of water contact compared to the 5- to 15-year-olds. A significant correlation between schistosomiasis and hematuria was established. Microhematuria showed a sensitivity of 80.6 %, a specificity of 92.7 %, and a positive predictive value of 61.7 %, whereas macrohematuria had a sensitivity of 47.2 %, a specificity of 99.2 %, and a positive predictive value of 89.5 %. The mass distribution of praziquantel in Burkina Faso is well established. However, over half of the participants with schistosomiasis in this study said they took praziquantel in the past 6 months, which indicates a high reinfection rate. This may be associated with a lack of knowledge about the transmission of schistosomiasis. Only 6 % of the participants in Kombissiri and 1.5 % in Dori knew about the correct mode of transmission. Conclusions The results of our study indicate that distribution campaigns should be extended from school-aged children to young women. Our data also demonstrate the necessity of combining already established mass distribution campaigns with information campaigns, so that long-term elimination, or at least reduction, of schistosomiasis can be achieved.