The 20-year war in northern Uganda has resulted in up to 1.7 million people being internally displaced, and impoverishment and vulnerability to violence amongst the civilian population. This qualitative study examined the status of health services available for the survivors of gender-based violence in the Gulu district, northern Uganda. Semi-structured interviews were carried out in 2006 with 26 experts on gender-based violence and general health providers, and availability of medical supplies was reviewed. The Inter-Agency Standing Committee (IASC) guidelines on gender-based violence interventions in humanitarian settings were used to prepare the interview guides and analyse the findings. Some legislation and programmes do exist on gender-based violence. However, health facilities lacked sufficiently qualified staff and medical supplies to adequately detect and manage survivors, and confidential treatment and counselling could not be ensured. There was inter-sectoral collaboration, but greater resources are required to increase coverage and effectiveness of services. Intimate partner violence, sexual abuse of girls aged under 18, sexual harassment and early and forced marriage may be more common than rape by strangers. As the IASC guidelines focus on sexual violence by strangers and do not address other forms of gender-based violence, we suggest the need to explore this issue further to determine whether a broader concept of gender-based violence should be incorporated into the guidelines.