In the Andes, as elsewhere, infanticide is a difficult challenge that remains largely undocumented and misunderstood. From January to March 2004 we used community-based vital event surveillance systems, discussions with health staff, ethnographic interviews, and focus group discussions among Aymara men and women from two geographically distinct sites in the Andes of Bolivia to provide insights into the practice of infanticide. We noted elevated mortality at both sites. In one location, suspected causes of infanticide were especially high for girls. We also observed that community members maintain beliefs that justify infanticide under certain circumstances. Among the Aymara, justification for infanticide was both biological (deformities and twinship) and social (illegitimate birth, family size and poverty). Communities generally did not condemn killing when reasons for doing so were biological, but the taking of life for social reasons was rarely justified. In this cultural context, strategies to address the challenge of infanticide should include education of community members about alternatives to infanticide. At a program level, planners and implementers should target ethnic groups with high levels of infanticide and train health care workers to detect and address multiple warning signs for infanticide (for example, domestic violence and child maltreatment) as well as proxies for infant neglect and abuse such as mother/infant separation and bottle use.