The operation of military courts is clearly allowed for and, in some cases, mandated by international humanitarian law (IHL). Nevertheless, the use of military courts has been one of the most controversial and hotly debated areas of human rights. Despite the ostensibly exclusive military domain, many human rights bodies have registered significant scepticism towards this type of justice. Consequently, they have sought actively to regulate this ‘IHL space’ with scant attention to the requirements of IHL itself. The article examines comments, case law, draft rules and other measures taken by two human rights frameworks: the United Nations Human Rights Council and the African Commission on Human and People’s Rights. It will analyse how, since 2000, these bodies have approached the issue of IHL when assessing the legitimacy and operation of military courts. For instance, do they consider IHL as a source of law guiding their efforts and rely on IHL instruments? How do they resolve conflicts between IHL and international human rights law? Additionally, the article will consider the validity, legality and effectiveness of these efforts. It concludes that, in reviewing military courts, there exists significant neglect of IHL in human rights frameworks. Through overlooking IHL or relegating it to a sub-specialty of international human rights law, these bodies not only ignore applicable law, they deprive themselves of the wealth of expertise found in commentary, debate, jurisprudence and practice in the IHL sphere. Instead, integrating IHL analysis and theory and affording it its appropriate respect within relevant human rights discussions will allow for greater legal and policy coherence, and human rights bodies will be better placed to fulfil their mandates.