BACKGROUND: This study explores the impacts of attacks perpetrated in the context of armed conflict, to female health workers in three Colombian territories. METHODS: We conducted a document review of the reports and databases of the Colombian Truth Commission, 17 in-depth semi-structured interviews with experts on the national and regional armed conflict and the medical mission, and 26 female health workers who were victims of attacks. RESULTS: Experts and female health workers reported attacks to health activities, facilities, equipment, and personnel, including attacks to traditional doctors belonging to indigenous communities. The most frequent attacks were threats and retention of health personnel; theft of supplies and medicines; damage and use of infrastructure and means of transport for purposes other than health care; and hinderance of health service provision. The attacks occurred in a framework of structural violence that intersects with poverty, racism, and gender bias. The impacts of these attacks include gender-based violence, significant disruption of the lives of health workers, and physical, emotional, psychological, social, and economic effects on the victims and their families. The government response to protect victims and populations has been absent or insufficient. CONCLUSIONS: Attacks to health care were reported in all the studied territories obstructing adequate health care. Impacts of these attacks affect negatively the professional and personal life of the workers and are aggravated by structural violence and absent or little institutional response.