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Aim Nonalcoholic fatty liver disease (NAFLD) is a leading cause of progressive and chronic liver injury. Complement factor 5a (C5a) may be involved in many inflammation disorders. This study investigated levels of systemic C5a in patients with and without NAFLD and lean controls. Methods A cross-sectional study was conducted from July 2012 to June 2013 among 96 Chinese children, aged 6-17 years, recruited from the Pediatric Department of the Second Affiliated Hospital of Xi'an Jiao Tong University: 40 obese children with NAFLD, 31 obese children without NAFLD and 25 lean controls. Anthropometric parameters, clinical data and circulating C5a levels were measured. Results Obese children had higher serum concentrations of complement factor C5a compared with lean controls, especially in obese children with NAFLD. C5a was positively correlated with body mass index (BMI), waist circumference, diastolic blood pressure (BP), triglycerides and homoeostasis model of insulin resistance, independent of their body mass index standard deviations score and age. Of the well-known risk factors, C5a was a significant predictor of NAFLD in obese children. Conclusion Serum C5a was elevated in obese children, especially in those with NAFLD and it may be proposed as a novel marker to predict advanced disease.