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Abstract Background Pesticides are identified as one of the dangerous poisons globally in children and are associated with increased short- and long-term morbidity. Pesticide poisoning is the most common method of self-poisoning among adults in rural Sri Lanka, and the clinical management is associated with significant healthcare costs to the country. There is however little data published on acute pesticide poisoning among children in rural Sri Lanka. The current study aimed to comprehensively evaluate clinical profiles, harmful first aid measures, emergency clinical management, complications and outcomes related to acute pesticide poisoning among children in the rural community of Sri Lanka. Methods This multicenter study was conducted in the North Central Province of Sri Lanka involving all children with acute pesticide poisoning and who were between 9 months and 12 years of age. Data were collected over 7 years (2007–2014), and children from 36 hospitals were recruited. Data collection was carried out by pretested, multi-structured, interviewer-administered questionnaires to identify clinical profiles of children, harmful first aid measures, emergency clinical management, reasons for delayed management, complications and outcomes of pesticide poisoning events. Results Among 1621 children with acute poisoning, 9.5% (155) comprised children with acute pesticide poisoning. Male children outnumbered female children, and the majority of children were less than 5 years. Most common pesticides implicated in poisoning of children were organophosphates and carbamates. Gastrointestinal and neurological symptoms were predominant clinical features. Limited transport and lack of concern regarding urgency among caregivers were leading reasons for delayed management. Most common location for poisoning was cultivation lands. Harmful first aid measures were practiced in 32.4%. 7.1% had intentional pesticide poisoning. The case fatality rate of all pesticide poisonings in the study was 1.9%. 58.1% of patients were transferred between regional hospitals and teaching hospital. Cardiac and respiratory arrests, aspiration pneumonia and convulsions were among the reported complications. Conclusions Acute pesticide poisoning in paediatric age group (