The aim was to determine the epidemiology and risk factors of childhood and young adult injuries among long-term Afghan refugees in Pakistan. A stratified cluster study was undertaken on a random sample of refugee households from June to July 2002. The Afghan Refugee Injury Survey was administered to the head of the household and recorded all injuries among household members within the last 3 months. Crude injury incidence was 12.3 per 1000 population among those aged 0-29 years (age groups 0-4, 5-14 and 15-29 years). Those aged 15-29 years had the highest injury rate (18.3 per 1000) closely followed by those aged 5-14 (12.3 per 1000) and much higher than the 0-4 years category (2.3 per 1000). Falls accounted for most injuries (48%) with both road traffic injuries and assaults accounting for 15%. The 15-29 year age group (odds ratio = 9.1) and those educated informally or for less than 6 years (odds ratio = 2.10), were associated with injury (p < 0.05) after adjustment for age, gender, occupation and education. Occupation was not associated with injury at a statistically significant level. Afghan refugee children and young adults are disproportionately affected by injuries, especially falls, than children in developed countries. Appropriate injury prevention strategies must be implemented among refugee camps with long-term refugees as part of their health programmes.