Colistin and polymyxin B are increasingly reintroduced in clinical practice due to the absence of effective antibiotics for the treatment of emerging infections caused by gram-negative bacteria. The synthesis of current evidence on the characteristics of polymyxins, especially regarding nephrotoxicity, is necessary. This study aims to conduct a systematic review and meta-analysis of cohort-type observational studies in order to identify the prevalence of nephrotoxicity in patients treated with either colistin or polymyxin B. PubMed, Scopus, and DOAJ electronic databases were searched, and manual searches were done. Cohort studies evaluating renal damage (nephrotoxicity) in adult patients caused by colistin or polymyxin B were included. Meta-analyses of the prevalence of nephrotoxicity as well as cumulative meta-analysis and meta-regression were conducted. After the systematic searches, 95 cohorts (n = 7911 patients) were included for analysis. The nephrotoxicity prevalence was 26.7% [confidence interval (CI) 95%: 22.8-30.9%] for colistin and 29.8% (CI 23.8-36.7%) for polymyxin B (P = 0.720). The publication year of the studies, the criteria used to classify renal damage, and the nephrotoxicity as primary or secondary outcome showed a significant influence on the adverse event rates.