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The aim of this study was to refine the population prevalence estimate of Tourette Syndrome (TS) in children and to investigate potential sources of heterogeneity in previously published studies. A systematic review was conducted and all qualifying published studies of TS prevalence were examined. Extracted data were subjected to a random-effects meta-analysis weighted by sample size; meta-regressions were performed to examine covariates that have previously been proposed as potential sources of heterogeneity. Twenty-six articles met study inclusion criteria. Studies derived from clinically referred cases had prevalence estimates that were significantly lower than those derived from population-based samples (P = 0.004). Among the 21 population-based prevalence studies, the pooled TS population prevalence estimate was 0.52% (95% confidence interval CI: 0.32-0.85). In univariable meta-regression analysis, study sample size (P = 0.002) and study date (P = 0.03) were significant predictors of TS prevalence. In the final multivariable model including sample size, study date, age, and diagnostic criteria, only sample size (P < 0.001) and diagnostic criteria (omnibus P = 0.003; Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, Text Revision [DSM-IV-TR]: P = 0.005) were independently associated with variation in TS population prevalence across studies. This study refines the population prevalence estimate of TS in children to be 0.3% to 0.9%. Study sample size, which is likely a proxy for case assessment method, and the use of DSM-IV-TR diagnostic criteria are the major sources of heterogeneity across studies. The true TS population prevalence rate is likely at the higher end of these estimates, given the methodological limitations of most studies. Further studies in large, well-characterized samples will be helpful to determine the burden of disease in the general population.