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Background Three different histological scores—histopathologic classification (Berden), Renal Risk Score (RRS) and the Mayo Clinic Chronicity Score (MCCS)—for anti-neutrophil cytoplasmic antibody (ANCA)-associated glomerulonephritis (ANCA-GN) were compared to evaluate their association with patient and kidney prognosis of ANCA-GN. Methods Patients aged >18 years with at least 1 year of follow-up and biopsy-proven ANCA-GN entered this retrospective study. Renal biopsies were classified according to Berden's classification, RRS and MCCS. The first endpoint was end-stage kidney disease (ESKD), defined as chronic dialysis or estimated glomerular filtration rate <15 mL/min/1.73 m2. The second endpoint was ESKD or death. Results Of 152 patients 84 were males, with median age of 63.8 years and followed for 46.9 (interquartile range 12.8–119) months, 59 (38.8%) reached the first endpoint and 20 died. The Kaplan–Meier curves showed that Berden and RRS were associated with first (Berden: P  = .004, RRS: P  < .001) and second (Berden: P  = .001, RRS: P  < .001) endpoint, MCCS with the first endpoint only when minimal + mild vs moderate + severe groups were compared (P  = .017), and with the second endpoint (P  < .001). Among the clinical/histological presentation features, arterial hypertension [odds ratio (OR) = 2.75, confidence interval (95% CI) 1.50–5.06; P  = .0011], serum creatinine (OR = 1.17, 95% CI 1.09–1.25; P  < .0001), and the percentage of normal glomeruli (OR = 0.97, 95% CI 0.96–0.99; P  = .009) were the independent predictors of ESKD at multivariate analysis. When the three scores were included in multivariate analysis, RRS (OR = 2.21, 95% CI 1.15–4.24; P  = .017) and MCCS (OR = 2.03, 95% CI 1.04–3.95; P  = .037) remained predictive of ESKD, but Berden (OR = 1.17, 95% CI 0.62–2.22; P  = .691) did not. Conclusion RRS and MCCS scores were independent predictors of kidney survival together with high serum creatinine and arterial hypertension at diagnosis, while Berden classification was not. [ABSTRACT FROM AUTHOR]