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Introduction Second-generation antipsychotics (SGAs) are widely used in the paediatric population. It is currently established that SGAs may induce metabolic adverse events (AEs) such as weight gain, perturbation of blood lipids or glucose with risk of potential cardiovascular morbidity and mortality. The Canadian Alliance for Monitoring Effectiveness and Safety of Antipsychotics in children (CAMESA) has published recommendations for monitoring the metabolic AEs of SGAs. Factors that may be associated with the onset of SGA’s metabolic AEs and long-term consequences are less studied in the literature. The objectives of our research are to evaluate some factors that can influence the development of the SGA’s metabolic AEs and to study clinical adherence to CAMESA guidelines.Methods and analysis The Monitoring des Effets Métaboliques des Antipsychotiques de Seconde Génération study is a multicenter, prospective, longitudinal observational study with repeated measures of metabolic monitoring over 24 months. Two recruiting centres have been selected for patients under 18 years of age, previously naive of antipsychotics, starting an SGA or who have started an SGA for less than 4 weeks regardless of the diagnosis that motivated the prescription. Assessments are performed for anthropometric measures, blood pressure, blood tests at baseline and 1, 2, 3, 6, 9, 12 and 24 months of follow-up.Ethics and dissemination The study protocol was approved by the CHU Sainte-Justine’s Research Ethics Board (MP-21-2016-1201) in 2016 and obtained institutional suitability for the ‘Centre Intégré Universitaire de Santé et de Services Sociaux du Nord-de-l’Île-de-Montréal’ Research Center in May 2018. For all participants, written consent will be obtained from parents/caregivers as well as the participant’s assent in order to enable their participation in this research project. The results of this research will be published.Trial registration number ClinicalTrials.gov (number NCT04395326).