Patients with microscopic colitis and patients with irritable bowel syndrome (IBS) present with similar symptoms. We examined the association between IBS and microscopic colitis in a systematic review and meta-analysis. We searched the medical literature to identify cross-sectional surveys or case-control studies reporting the association between microscopic colitis and IBS in 50 or more unselected adult patients. We recorded the prevalence of IBS symptoms in patients with histologically confirmed microscopic colitis, or the prevalence of histologically confirmed microscopic colitis in patients with IBS. Data were pooled using a random-effects model; the association between microscopic colitis and IBS was summarized using an odds ratio (OR) with a 95% confidence interval (CI). The search strategy identified 3926 citations, of which 10 were eligible for our analysis. The pooled prevalence of IBS in patients with microscopic colitis was 33.4% (95% CI, 31.5%-40.6%), but was not significantly higher in patients with microscopic colitis than in patients with diarrhea (OR, 1.39; 95% CI, 0.43-4.47). In 3 cross-sectional surveys, the pooled OR for microscopic colitis in participants with IBS, compared with other patients with diarrhea, was 0.68 (95% CI, 0.44-1.04). In 4 case-control studies the prevalence of IBS in patients with microscopic colitis was significantly higher than in asymptomatic controls (OR, 5.16; 95% CI, 1.32-20.2). Based on a meta-analysis, one third of patients with microscopic colitis reported symptoms compatible with IBS, but the prevalence of IBS was no higher than in other patients with diarrhea. The odds of microscopic colitis were no higher in patients with IBS compared with other patients with diarrhea. The value of routine colonoscopy and biopsy to exclude microscopic colitis in patients with typical IBS symptoms, unless other risk factors or alarm symptoms are present, remains uncertain.