In the 1980s, villages in the Kurdistan region of Iraq were exposed to chemical weapons (CWs), which killed and injured thousands of civilians. There has been no clinical assessment of the long-term effects of CWs exposure on those injured. We report the first such evaluation of CW effects on long-term health of children. Patients from the CW-exposed areas were interviewed to assess previous and current clinical history and underwent clinical examination. The status of organs known to be targets of CWs, including skin, eyes, respiratory and neuromuscular systems, was assessed. Children of similar age and social background, but with no history of CW exposure, were selected as a control population. Results showed that 70% of children in the CWs group had chronic health problems in contrast to 3.3% in the unexposed group (p < 0.0001). Fifty-five per cent of the CW-exposed group had long-term visual impairment but none in the unexposed population. Thirty-six per cent of the CW-exposed group had chronic dermatological conditions compared with 0.8% of the unexposed group (p < 0.0001), 31% of the CWs group had neurological sequelae compared with 0.4% of the unexposed group (p < 0.0001) and 51% of the CWs group had long-term respiratory problems compared with 1.5% of the unexposed group (p < 0.0001). Respiratory complaints including asthma, chronic bronchitis and bronchiectasis were particularly common. Our study suggests that CWs used were probably a combination of sulphur mustard and organophosphate nerve agents. Results also indicate that the prevalence of acute and chronic health problems following exposure to CW agents appear to be higher in children compared with reported data in adults.