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The objective of the present study was to determine the prevalence of chronic fatigue syndrome (CFS) and its associated factors in middle-school students in Suzhou, China. From September 2010 to January 2011, across-sectional study was conducted in junior- and senior middle-school students aged 10 to 18 years using a battery of confidential questionnaires. Our results indicate that 18,139 completed the questionnaires effectively, of whom 163 (0.9%) met the definition of CFS, with senior high-school students and male students predominating. The prevalence of CFS in the middle-school students increased steadily with age. The main symptoms of CFS in these students included being afraid of going to school, despondency, and irritability in addition to those specified in the Centers for Disease Control and Prevention (CDC). Our study shows that CFS is prevalent among Chinese teenagers, and requiring proper intervention and treatment.