Two decades of conflict in northern Uganda have had a devastating impact on the lives of thousands of civilians. Like so many of today’s ‘dirty wars,’ gender-related crimes have been pervasive. While numerous disciplines over the past century have developed sophisticated theories for understanding the nature and agency surrounding sexual offences, the nascent field of transitional justice is only just beginning to grapple with these issues or design appropriate measures of redress. This paper is based on research undertaken to look at issues of gender-based violence (GBV) in four camps for the internally displaced in northern Uganda in order to provide insight into the nature and prevalence of GBV within a specific context. The findings show that specific GBV dynamics need to be scrutinised within zones of conflict and taken into consideration in the policies adopted post-conflict. The paper both illuminates the nature of such abuses within the Ugandan context and points to the need for concerted attention to be paid to the pervasive gender dimensions of violence when designing transitional justice mechanisms.