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Quality of life (QoL) in children with inflammatory bowel disease (IBD) is often impaired by underlying disease. We evaluated factors affecting health-related QoL (HRQoL) in Malaysian children with IBD.A cross-sectional study using IMPACT-III questionnaires evaluating HRQoL in children aged 8-17 years with duration of IBD of ≥6 months was conducted. IMPACT-III, a validated instrument designed to measure HRQoL in children with IBD, was used. Higher IMPACT-III (maximum = 100) score indicates better HRQoL. Impact of socio-demographic and clinical factors of IBD on the HRQoL was evaluated. Paediatric Crohn's disease (CD) and ulcerative colitis (UC) activity indices were used to classify disease severity.A total of 75 children (UC = 44, CD = 41; mean (SD) age at diagnosis 8.2 (3.5) years) were interviewed at mean age of 12.8 (2.7) years. Mean IMPACT-III score was significantly lower in children with more severe disease (mild: 71.8 (13.6) vs. moderate: 65.5 (10.9) vs. severe: 46.3 (14.5); P 0.001), history of hospitalisation (yes: 64.0 (14.0) vs. none: 74.1 (12.2), P = 0.034) and a higher number of admissions (r = -0.352, P = 0.041) in preceding 6 months. Diagnosis at a younger age (r = -0.31, P = 0.007) and a longer duration of disease (r = 0.286, P = 0.013) was associated with higher score. A higher weight-for-age (r = 0.261, P = 0.023) or body mass index-for-age z-score (r = 0.235, P = 0.042) was correlated with a better body image domain score, respectively.In Malaysian children with IBD, HRQoL was adversely affected by a more severe disease. Better control of disease activity and maintaining long-term remission are important to improve the HRQoL in childhood IBD.