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Anal fissures are a common problem and have a cumulative lifetime incidence of 11%. Previous reviews on anal fissures show inconsistent results regarding post-interventional healing and incontinence rates. In this review our aim was to compare the treatments for chronic anal fissures by incorporating indirect comparisons using network meta-analysis. The PubMed database was searched for randomized controlled trials (RCTs) published between 1975 and 2015. The primary outcome measures were healing and incontinence rates after lateral internal sphincterotomy (LIS), anal dilatation (DILA), anoplasty and/or fissurectomy (FIAP), botulinum toxin (BT) and noninvasive treatment (NIT). Random effects network meta-analyses were complemented by fixed effects and Bayesian models. The present analysis included 44 RCTs and 3268 patients. After a median follow-up of 2 months, the healing rates for LIS, DILA, FIAP, BT and NIT were 93.1, 84.4, 79.8, 62.6, and 58.6% and the incontinence rates were 9.4, 18.2, 4.9, 4.1, and 3.0%, respectively. Compared with NIT, the odds ratio (OR) [95% confidence interval (CI)] for healing after LIS, DILA, FIAP and BT was 9.9 (5.4-18.1), 8.6 (3.1-24.0), 3.5 (1.0-12.7) and 1.9 (1.1-3.5), respectively, on network meta-analysis. The OR (95% CI) for incontinence after LIS, DILA, FIAP and BT was 6.8 (3.1-15.1), 16.9 (6.0-47.8), 3.9 (1.0-15.1) and 1.6 (0.7-3.7), respectively. Ranking of treatments, fixed effects and Bayesian models confirmed these findings. In conclusion, based on our meta-analysis LIS is the most efficacious treatment but is compromised by a high rate of postoperative incontinence. Given the trade-offs between the risks and benefits, FIAP and BT might be good alternatives for the treatment of chronic anal fissures.