Violence against women, especially by intimate partners, is a serious public health problem that is associated with physical, reproductive, and mental health consequences. The effect of intimate partner violence on women's ability to control their fertility and the mechanisms through which these phenomena are related merit further investigation. Building on findings from a previous analysis in which a statistically significant relationship between intimate partner violence and unintended pregnancy in Colombia was found, this analysis examines the effect of gender inequality on this association using data from the 2000 Colombian Demographic and Health Survey. Specifically, the objective of this analysis is to explore whether gender inequality (as measured by women's autonomy, women's status, male patriarchal control, and intimate partner violence) in municipalities partially explains the association between intimate partner violence and unintended pregnancy in Colombia. Results of logistic regression analysis with multi-level data show that living in a municipality with high rates of male patriarchal control significantly increased women's odds of having an unintended pregnancy by almost four times. Also, living in a municipality with high rates of intimate partner violence increased one's odds of unintended pregnancy by more than 2.5 times, and non-abused women living in municipalities with high rates of intimate partner violence were at a significantly increased risk of unintended pregnancy. In addition, abused women living in a municipality with high personal female decision-making autonomy had more than a fourfold increased risk of having an unintended pregnancy. These findings demonstrate the need for reproductive health programs to target areas at particularly high risk for unintended pregnancy by reducing intimate partner violence and gender inequality.