INTRODUCTION: Microscopic colitis (MC) is an inflammatory bowel disease of the colon that presents with chronic watery diarrhea. These patients have many risk factors for osteoporosis including female predominance, mean age in the 60s, lower body-mass index (BMI) and active smoking. Additionally the mainstay of therapy is a corticosteroid, budesonide. Bone density has not been rigorously studied in the population. Our aim was to evaluate for bone mineral density in patients with a diagnosis of MC with and without the use of corticosteroids. METHODS: We queried our prospective MC patient registry at NorthShore University HealthSystem, a clinical database of biopsy-confirmed patients with MC. Patients were included if they had a dual energy X-ray absorptiometry (DEXA) scan. DEXA measurements of the radius, femoral neck, and lumbar spine were used to evaluate bone mass. Baseline clinical factors were also collected, particularly tobacco use, BMI, and treatments for MC including corticosteroids. In this case-control study, age and gender-matched controls without diarrhea served as the control population. RESULTS: Of the 192 subjects in our registry, only 94 patients had undergone or had available bone density evaluations. The mean age at diagnosis was 69 years (range 42–91), with 91% female. No significant difference in rates of osteoporosis or osteopenia was observed in patients with MC (OR 1.58 [95% 0.75–3.30, P = 0.22]). Bone loss, defined as osteopenia or osteoporosis, was present in 82% of MC patients, compared to 75% in the controls. 76% of patients with MC received prolonged treatment with budesonide, and 24% received no steroids. A significant difference in bone mass was not appreciated between MC patients treated with a steroid, compared to controls (OR 1.15 [95% 0.33–4.03, P < 0.83]). CONCLUSION: Patients with MC have increased rates of osteopenia or osteoporosis compared to controls. However, our control cohort had a significantly higher degree of bone loss than current US estimates of 45–55%, which likely affected our statistical significance. Thus, bone loss is an underappreciated but important problem in microscopic colitis. With increased awareness, DEXA scans should be performed routinely in MC patients, particularly in those who have known risk factors for osteoporosis.