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Lack of data on traumatic brain injuries (TBI) hinders the appreciation of the true magnitude of the burden, and poses a barrier to defining risks, vulnerable groups, and the impact of potential interventions. This work describes a scientific approach for hospital based systematic data collection in a low-income country (LIC), and details the steps of developing an internet-based TBI registry in Uganda. The registry is developed and implemented based on the evaluation framework for injury surveillance systems (EFISS) which comprises a four-step approach: (1) identifying characteristics that assess a surveillance system, (2) a thorough review of the identified characteristics(variables) based on adopted Specific, Measurable, Achievable, Realistic, Time-bound (SMART) criteria, (3) assessment of the proposed variables and system characteristics by an expert panel, and (4) development and application of a rating system. After extensive literature review on TBI surveillance and management, variables and implementation strategy were finalized by a peer review panel and an mHealth platform was developed for data collection in Mulago Hospital, Kampala. The TBI registry is designed to capture comprehensive, yet context-specific, information on each case, from the time of injury until death or discharge from the hospital, with a cut off at 30 days if the patient was still admitted. It included patients’ demographic information, pre-hospital and hospital assessment and care, causes of TBI, injury severity, and patient outcomes in terms of survival and disability. This was the first mHealth based TBI registry to be pilot tested in a tertiary care hospital of Uganda. An mHealth-based TBI registry in Uganda will open the opportunity to replicate the process in similar context and thus contribute to a better understanding of TBI in these settings, and feed into the global agenda of reducing deaths and disabilities from TBI in low-and middle-income countries.