Clinical evidence reflecting the recent development of treatments for patients with critical limb ischemia is mandatory to guide the decision-making process for the selection of revascularization procedures, including bypass or endovascular treatment. This paper describes the protocol for a clinical study that is designed and carried out by both vascular surgeons and interventional cardiologists collaboratively, and will investigate current treatment for critical limb ischemia in Japan. The registry aimed to recruit approximately 450 patients with critical limb ischemia, including approximately 150 patients who underwent bypass surgery and approximately 300 patients who underwent endovascular treatment in 23 institutions. The primary endpoint of this study is amputation-free survival at 36 months, and the secondary endpoints include major amputation, cardiovascular events, re-intervention, death, ulcer healing, and their composite outcomes. The SPINACH study aims to provide a suitable patient model for each revascularization procedure, bypass and endovascular treatment, and will expound on the role of each approach for critical limb ischemia treatment (Clinical trial registration UMIN000007050).