Microscopic colitis (MC), encompassing lymphocytic and collagenous colitis, is a common cause for chronic nonbloody diarrhoea, which impacts significantly on the quality of life for patients. Despite increasing awareness of the condition and its treatment, there is considerable variation in therapeutic approaches. To conduct a systematic review and meta-analysis on the efficacy and safety of budesonide in the treatment of MC. We searched Medline, Embase and Central databases using predefined search methodology for randomised trials using budesonide in the treatment of MC. We extracted data, on the efficacy and safety of budesonide, from studies identified that met the feasibility for analysis criteria. These data were pooled with a fixed effects model. Nine studies met the inclusion criteria for analysis. The pooled odds ratios (ORs) for a response to budesonide therapy at induction and maintenance were 7.34 [95% confidence interval (CI): 4.08-13.19] and 8.35 (95% CI: 4.14-16.85) respectively. Histological response rates were superior in budesonide-treated patients compared to placebo following induction (OR: 11.52; 95% CI: 5.67-23.40) and maintenance treatment (OR: 5.88; 95% CI: 1.90-18.17). There was no difference in adverse events. Significant relapse rates (>50%) were observed following treatment cessation with no difference noted between the budesonide or the placebo-treated patients. Budesonide is an effective treatment option for MC for achieving induction and maintenance of both clinical and histological response. High relapse rates on treatment cessation were observed.