OBJECTIVE Microscopic colitis has been associated with celiac disease. We aimed to determine the extent and significance of this relationship. METHODS A prospectively maintained database of celiac disease patients, seen between 1981 and 2006, was analyzed. Standardized morbidity ratios (SMR) were calculated using a general population study of microscopic colitis as the reference group. Statistical analysis was conducted using the Student t test, Pearson chi(2) test, or Fisher exact test. RESULTS Microscopic colitis was found in 44 of 1009 patients (4.3%); this represented a 70-fold increased risk for individuals with celiac disease to have microscopic colitis, compared with the general population (SMR, 72.39; 95% confidence interval [CI], 52.52-95.36). The celiac disease patients with microscopic colitis were older (P = .0001) and had more severe villous atrophy (P = .002) than the celiac disease patients without microscopic colitis. Microscopic colitis was diagnosed after celiac disease in 64% of the patients, simultaneously in 25%, and before celiac disease in 11% (P = .0001). Pancolitis predominated, though 16% had colitis limited to the right colon. Steroid or immunosuppressant therapies were required in 66% of the celiac disease patients with microscopic colitis and given as maintenance therapy to 50% of these patients. Follow-up biopsies revealed that the colitis persisted in 57% of the patients with celiac disease and microscopic colitis, despite improved diarrhea symptoms; the diarrhea resolved in most of the patients. CONCLUSIONS Microscopic colitis is more common in patients with celiac disease than in the general population. Patients with celiac disease and microscopic colitis have more severe villous atrophy and frequently require steroids or immunosuppressant therapies to control diarrhea.