The aim of this study was to identify the prevalence and severity of intimate partner violence (IPV) in eight indigenous regions of Mexico, as well as the socioeconomic and demographic variables that are associated with this phenomenon. A cross-sectional study was conducted in indigenous regions that have a greater availability of government medical services than other indigenous regions. Interviews were conducted with female patients (n = 3287) seeking medical care in either of the two public health institutions in these regions. The severity of intimate partner violence (SIPV) during the previous 12 months was measured using a 33-item scale. Multinomial logistic regression analyses were performed to explore the factors associated with SIPV. Intimate partner violence prevalence was 25.5% (95%CI 24.93–25.26). Female partner variables such as personal history of child abuse (ORA 3.48; 95%CI 2.48–4.89) and work outside the home (ORA 1.74; 95%CI 1.22–2.49) and male partner variables such as unemployment (ORA 2.31; 95%CI 1.34–3.97) and a high frequency of alcohol use (ORA 13.35; 95%CI 7.02–25.39) were the main predictors for IPV. We found a three-fold higher risk of IPV for women living in the Los Altos de Chiapas region (ORA 3.01; 95%CI 1.88–4.79) compared with women in the Mayan region (reference category). Such results should aid decision makers in the development of extended public policies and interventions to address violence against women in the indigenous populations of Mexico.