The polymorphism +49A/G in the cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) gene has been implicated in susceptibility to Hashimoto's thyroiditis (HT), but the findings are not clear-cut. This study aimed to investigate the association between CTLA-4 polymorphisms and HT risk using an updated meta-analysis. A meta-analysis was carried out of 14 previous studies that investigated the CTLA-4 +49A/G polymorphism and HT risk. +49A/G was associated with a significantly increased HT risk in both allele analysis and all genetic models (allele analysis: G vs. A: P < 0.001, OR = 1.379, 95 % CI = 1.244-1.529). Subgroup analysis by ethnicity showed a significantly increased HT risk with the G allele and all other genetic models in the Asian subgroup (P < 0.001). In the Caucasian subgroup, no significant association was detected between the CTLA-4 +49 G allele and HT, or in the genetic model analysis (P = 0.05). This gene-based analysis indicates that the cumulative effect of the +49A/G polymorphism in CTLA-4 is associated with HT in Asians, but appears to have no effect on HT in Caucasians.