Background: Hashimoto's thyroiditis is an autoimmune thyroid disorder. Lymphocytic colitis and collagenous colitis are characterized by diarrhea with normal endoscopic findings. Autoimmune disorders are common in Hashimoto's thyroiditis and lymphocytic colitis. The aim of this study was to investigate the incidence of lymphocytic colitis in patients with Hashimoto's thyroiditis. Study: Fifty patients with well-documented Hashimoto's thyroiditis were included. Twenty patients with nonulcer dyspepsia served as a control group. Five of 50 patients with Hashimoto's thyroiditis reported intermittent diarrhea, whereas no patients had diarrhea in the control group. All patients and the control group underwent total colonoscopy, and multiple colonoscopic biopsies were performed. Results: We found that 40% (20 of 50) of Patients with Hashimoto's thyroiditis had histologic findings consistent with lymphocytic colitis, and one patient in the control group had lymphocytic colitis (p < 0.01). The mean number of intraepithelial lymphocytes was 34.4/100 epithelial cells in these 20 patients, whereas the mean number of intraepithelial lymphocytes was 12.3/100 epithelial cells in the other 30 patients with Hashimoto's thyroiditis (p < 0.05). Conclusions: There was a higher incidence of histologic findings of lymphocytic colitis in patients with Hashimoto's thyroiditis, although most of the patients were clinically asymptomatic. This finding suggests that lymphocytic colitis may have an asymptomatic clinical course and should encourage further clinical investigations to better anticipate the relationship between autoimmune disorders.