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Background Following a finding of alcohol use among children aged 5–8 years old in Mbale, Uganda, this project investigates the magnitude of alcohol and substance use among children ged 6–13 years old and related household, community, school, health system and clinical factors.Methods The project includes four larger work packages (WPs). WP1 comprises management, WP2 and 3 include the scientific components and WP4 includes integration of results, dissemination, policy and implementation advice. This protocol presents the planned research work in WP 2 and 3. WP2 comprises the adaptation and validation of the alcohol use screening tool Car-Relax-Alone-Forget-Family and Friends-Trouble (CRAFFT) to the age group and setting. WP3 comprises four substudies (SS). SS1 is a cross-sectional community household survey with an estimated sample size of 3500 children aged 6–13 years and their caregivers. We apply cluster sampling and systematic sampling within the clusters. Data collection includes a structured questionnaire for caregiver and child, measuring social and demographic factors, mental health status, alcohol and substance use, nutrition history and anthropometry. Urine samples from children will be collected to measure ethyl glucuronide (EtG), a biological marker of alcohol intake. Further, facilitators, barriers and response mechanisms in the health system (SS2) and the school system (SS3) is explored with surveys and qualitative assessments. SS4 includes qualitative interviews with children. Analysis will apply descriptive statistics for the primary outcome of establishing the magnitude of alcohol drinking and substance use, and associated factors will be assessed using appropriate regression models. The substudies will be analysed independently, as well as inform each other through mixed methods strategies at the stages of design, analysis, and dissemination.Ethics and dissemination Data protection and ethical approvals have been obtained in Uganda and Norway, and referral procedures developed. Dissemination comprises peer-reviewed, open access research papers, policy recommendations and intersectoral dialogues.Trial registration numberClinicaltrials.gov 29.10.2020 (#NCT04743024).