Abstract Background The Health in Prisons European Database (HIPED) aims to periodically collect data on prison health systems, services and health outcomes to inform equivalence of care for people living in prison. Recognized as the United Nations hub for health data in prisons, HIPED lacked an established framework to define its domains and indicators to measure progress. Therefore, the objectives of developing this framework were to inform surveillance systems at prison, local, regional, national and international level and to use it to guide improvement of prison health systems and cross-country comparison. Methods The framework was conceptualized through identification of policy priorities and existing frameworks, notably the WHO Health System Framework. A consultation with a range of WHO stakeholders was conducted evaluating the components of existing frameworks and their relevance to the prison health context, as well as identifying areas needing further emphasis. The final stage identified the structure of the framework. Results The framework consists of three main building blocks. The first captures the system-level aspects of prison health care (or inputs) whilst the second captures delivery aspects of prison health care (or outputs). These building blocks are in turn modified by two influencing factors. Ultimately, all these elements impact on the third building block, health outcomes. In addition, two cross-cutting principles associated with all these building blocks and influencing factors are included. Conclusions A new framework for assessing prison health system performance is now available, crucial to support informed decision-making for policy design and implementation for prisons and other places of detention.