Background: Helicobacter pylori infection is reportedly associated with extradigestive diseases such as immune thrombocytopenic purpura and coronary heart disease. The risk factors for autoimmune thyroid diseases (ATDs) remain largely unknown, and whether H. pylori infection is associated with ATDs is still controversial. The aim of this meta-analysis was to determine the association between H. pylori infection and ATDs. Methods: Studies comparing the prevalence rate of H. pylori infection in patients with ATDs and healthy controls, published in English, were identified through a systematic search in MEDLINE and EMBAS up to June 2012. Serological or nonserological tests were used to confirm H. pylori infection and the presence of cytotoxin-associated gene A ( CagA ) antigens. The odds ratios (OR) and associated 95% confidence intervals [CI] were obtained. Results: Seven studies involving a total of 862 patients met the inclusion criteria and thus were included in our meta-analysis. Overall, H. pylori infection was associated with ATDs (OR 1.92 [CI 1.41–2.61]); the association was significant for Graves' disease (OR 4.35 [CI 2.48–7.64]) but not for Hashimoto's thyroiditis (OR 1.45 [CI 0.92–2.26], p =0.11). No association was observed in the subanalysis of studies using only enzyme-linked immunosorbent assay to detect H. pylori infection (OR 1.38 [CI 0.86–2.19], p =0.18). Five of the seven articles reported the association of CagA seroprevalence and ATDs. CagA seropositivity significantly increased the risk for ATDs by 2.24-fold [CI 1.06–4.75]. Conclusions: Both the prevalence of H. pylori infection and the seroprevalence of CagA -positive strains are associated with ATDs. These findings suggest that H. pylori infection potentially plays a part in the development of ATDs.