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Constipation is a common childhood disease. It is associated with exposure to stressful events. Sri Lanka was involved in three decades of civil war causing significant emotional stress. This study assessed the prevalence of childhood constipation during and after war. Data were collected from 10- to 16-year olds in five randomly selected schools, in three provinces (two schools from Eastern province), using a validated, self-administered questionnaire. Constipation was diagnosed using Rome III criteria. Phase I was conducted during the war to liberate Eastern province from separatist groups. Phase II was conducted 2 years after the war in same schools. During Phase I, prevalence of constipation was significantly higher in Eastern province (18.1%) compared with Western (14.2%) and Southern (12.6%) provinces (p = 0.009). Constipation was significantly lower in Eastern province in Phase II (10%) compared with Phase I (p < 0.0001). This study highlights the possible link between devastating emotional effects of civil war and childhood constipation.