Infection caused by Helicobacter pylori is considered as a serious health issue as it can cause severe damage of gastric mucosa, impair the digestive mechanism and even lead to neoplastic disease. Research studies have projected its survival in many parts of the body beyond the gastric system. The ability of these bacteria to withstand the gastric juice and change the surrounding conditions makes its survival in the stomach successful. As an outcome of H. pylori infection, there occurs the release of inflammatory mediators and immune modulators, which could cause further complications. Recent investigations on H. pylori have demonstrated the association of its infection with many systemic diseases including lung cancer, urticaria, type-1 diabetes, autoimmune diseases and so on. Autoimmune thyroiditis (AIT) is an organ-specific autoimmune disease, which occurs as a result of production of autoantibodies to thyroid gland leading to thyroid dysfunction. Antibodies of similar kind produced against H. pylori have been demonstrated for their occurrence in patients suffering with AIT in many studies. On the other hand, some of the studies have experimentally proved the lack of link between H. pylori infection and AIT. As the findings attributing H. pylori infection with the AIT are increasingly reported in recent years, this article reviews the concepts and controversies over their association.