Abstract Background Hashimoto thyroiditis (HT) is the most common autoimmune disease worldwide, characterized by chronic inflammation and circulating autoantibodies against thyroid peroxidase and thyroglobulin. Patients require hormone replacement with oral levothyroxine, and if untreated, they can develop serious adverse health effects and ultimately death. There is a lot of evidence that the intestinal dysbiosis, bacterial overgrowth, and increased intestinal permeability favor the HT development, and a thyroid–gut axis has been proposed, which seems to impact our entire metabolism. Aim of the Work To Study the Correlation of stool lactobacillus acidophilus and leaky gut syndrome in patients with hashimoto thyroditis. Patients and Methods This was a case control study that was conducted on 60 Egyptian patients that was divided into 2 groups, Group 1 that included 30 patients with Hashimoto s thyroiditis first diagnosed or on therapy and Group 2 that included 30 healthy subjects as a control and it was conducted at Ain Shams University hospital outpatient Endocrinology Clinic throughout 6 months. Results There was no statistically significant difference between two groups regarding Gender and Age, and there was highly statistically significant difference found between two groups regarding BMI. There was no statistically significant difference found between two groups regarding FT3, and there was highly statistically significant difference found between two groups regarding FT4 and TSH. There was highly statistically significant difference found between two groups regarding Anti tpo, Zonulin and Lactobacillus PCR. There was non statistically significant difference found between two groups regarding Gender, Age and BMI. No statistically significant difference was found between two groups regarding FT3, FT4 and TSH. There was highly statistically significant difference found between two groups regarding Anti tpo, and there was no statistically significant difference found between two groups regarding Zonulin. Conclusion There are alterations in the micro biota and intestinal permeability in Brazilian patients with HT. In addition, we suggest that diet might have played an important role in modulating the gut micro biota in patients with HT. These findings could help understand the HT development and progression, while.