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Objective To assess the rural–urban disparity in caesarean section rates using electronic health records from hospitals located in the Province of Inner Mongolia, which is a minority area in Northeastern China.Methods The study examined the electronic health records of women that gave birth in three major public hospitals between January 2012 and December 2016. Multinomial regression analyses were used to estimate rural–urban disparities in caesarean section rates.Results Data from 61 903 women were examined. Caesarean section rates increased slightly over the study period and the rate was significantly higher in rural compared with urban hospitals (48% versus 38%). This disparity consistently increased over time. Multinomial regression analyses showed that maternal age, ethnicity, health insurance type, employment status, reproductive history and the newborn’s sex were significant risk factors associated with caesarean section rate. Furthermore, stratified analysis of first-time pregnancies, minorities and different age groups showed that the odds of undergoing an emergency caesarean section was lower in the rural hospital, but the odds of undergoing a planned caesarean section was higher in the rural hospital.Conclusions Caesarean section rates have increased in rural areas and the disparity in rural–urban areas has increased substantially over the years.