This article examines the protection of the rights of women and LGBTQI+ (lesbian, gay, bisexual, transgender, queer, intersex) individuals in detention through the case law of the European Court of Human Rights. While the vast majority of rulings on detention conditions concern men, women and LGBTQI+ individuals remain largely invisible in Strasbourg’s prison-related litigation and the accompanying legal doctrine. The analysis focuses particularly on two major issues in European case law regarding the treatment of these populations: motherhood in detention and the isolation and segregation of LGBTQI+ individuals within penitentiary institutions.