The purpose of this study was to describe the state of rehabilitation health information systems (HIS) in different settings, and identify key processes and actions which contribute to the development of HIS which can effectively support low- and middle-income countries (LMICs) allocate resources to health-related rehabilitation to people with disabilities. Nine case studies were conducted across different disability and developmental settings using documentary review and semi-structured key informant interviews (N = 41). Results were analysed against the six building blocks of a HIS, based on the Health Metrics Network Framework and Standards for Country Health Information Systems and existing HIS capacity. Key barriers or enablers to good disability data collection and use, were documented for each HIS component. Research results suggest there is no gold standard HIS for rehabilitation. There was broad consensus however, that effective health related disability planning requires reliable data on disability prevalence, functional status, access to rehabilitation services and functional outcomes of rehabilitation. For low-resource settings, and where routine HIS are already challenged, planning to include disability and rehabilitation foci starting with a minimum dataset on functioning, and progressively improving the system for increased utility and harmonization, is likely to be most effective and minimize the potential for overburdening fragile systems. The recommendations from this study are based on the successes and challenges of countries with established information systems, and will assist LMICs to prioritize strategic measures to strengthen the collection and use of data for rehabilitation, and progressively realize the rights of people with disabilities.