Background: this study examined fermented food consumption habits and the relationship between other factors and Hashimoto’s thyroiditis (HT) Methods: the study included 90 children and their mothers, 45 of whom had HT and 45 of whom did not. Participants answered a survey questioning about their fermented food consumption habits and the status of various environmental factors. Results: mothers who consumed homemade pickles during pregnancy (OR: 0.341 [95 % CI: 0.117 to 0.990]) homemade yogurt (OR: 0.091 [95 % CI: 0.011 to 0.752]), tarhana (OR: 0.325 [95 % CI: 0.136 to 0.778)]) and olive oil (OR: 0.163 [95 % CI: 0.033 to 0.792]) were found to have a statistically significant lower risk of developing Hashimoto’s disease in their children. The risk of HT in children who consumed homemade yogurt (OR: 0.091 [95 % CI: 0.011 to 0.752]), cheese (OR: 0.242 [95 % CI: 0.100 to 0.590]), and olive oil (OR: 0.042 [95 % CI: 0.002 to 0.750]) was found to be significantly lower than in children who did not consume it. Conclusions: fermented food consumption habits can be protective against autoimmune diseases such as HT by affecting the immune system through the intestinal microbiota.