Background: Helicobacter Pylori (H. Pylori) usually acquired in childhood, it colonizes the gastric mucosa of about 50% of the world's population at some time in their life. In eastern countries, H. pylori infection has a prevalence of approximately 70%. Objective: To correlate between H. pylori infection and autoimmune thyroid diseases (AITD). Patients and Methods: This is a cross-sectional study done on 200 patients selected as a convenient sample with upper GI upset. They were selected from gastroenterology outpatient clinics at Al-Hussein and Alexandria Police Hospitals, during the summer months of 2018. They were classified according to the results of stool H. pylori Ag testing into two groups; positive and negative (each group 100 patient). This is cross-sectional study done on 200 patients selected as a convenient sample Results: Our results indicated that patients with H. pylori infection were more susceptible to AITD. There was significant association between H. pylori infection and both Hashimoto's and Graves' disease. H. pylori infection had shown to be associated with elevated liver enzymes, anemia, and IL 17. Conclusion: There is a significant positive relationship between H. pylori infection and Hashimoto's disease (HT). There is a significant positive relationship between H. pylori infection and Graves' disease (GD).