BEST-CLI, an international randomised trial, compared bypass surgery with endovascular treatment in chronic limb threatening ischaemia (CLTI). In this substudy, overall amputation rates and risk of major amputation as an initial or subsequent outcome were evaluated. A total of 1 830 patients were randomised to receive surgical or endovascular treatment:(1) patients with adequate single segment great saphenous vein (SSGSV) (n = 1 434); and (2) patients without adequate SSGSV (n = 396). Differences in time to first event and number of amputations were evaluated. In cohort 1, 410 (45.6%) total amputation events occurred in the surgical group vs. 490 (54.4%) in the endovascular group (p = .001) during mean follow up of 2.7 years. Every third patient underwent minor amputation after index revascularisation: 31.5% of the surgical group vs. 34.9% in the endovascular group (p = .17). Subsequent major amputation was required significantly less often in the surgical group compared with the endovascular group (15.0% vs. 25.6%; p = .002). The first amputation was major in 5.6% of patients in the surgical and 6.0% in the endovascular group (p = .72). Major amputation was required in 10.3% (n = 74/718) of patients in the surgical group and 14.9% (n = 107/716) in the endovascular group (p = .008). In cohort 2, 199 amputation events occurred in 132 (33.3%) patients during mean follow up of 1.6 years: 95 (47.7%) in the surgical vs. 104 (52.3%) in the endovascular group (p = .49). Major amputation was required in 15.2% (n = 30/197) of the patients in the surgical and 14.1% (n = 28/199) in the endovascular group (p = .74). In patients with CLTI, surgical bypass with SSGSV was more effective than endovascular treatment in preventing major amputations because of a decrease in major amputations subsequent to minor amputations.