DYX1C1 and KIAA0319 have been two of the most extensively studied candidate genes for dyslexia given their important roles in the neuronal migration and neurite growth. The −3G > A in DYX1C1 and the 931C > T in KIAA0319 were of special interest for dyslexia but with inconsistent results. We performed a meta-analysis integrating case–control and transmission/disequilibrium test (TDT) studies to clearly discern the effect of these two variants in dyslexia. Data from case–control and TDT studies were analyzed in an allelic model using the Catmap software. In overall meta-analysis, the pooled OR for the −3A allele and the 931T allele was 0.68 (95% CI = 0.25–1.87, Pheterogeneity = 0.000) and 0.87 (95% CI = 0.78–0.98, Pheterogeneity = 0.125), respectively. The stratified analysis showed that the between-study heterogeneity regarding the −3G > A polymorphism might be accounted by the publication year. Additionally, the sensitivity analysis of −3G > A polymorphism indicated the stability of the result. In conclusion, our results suggested that the 931C > T variant in KIAA0319, but not the −3G > A in DYX1C1, was significantly associated with the risk of dyslexia. © 2012 Wiley Periodicals, Inc.