Background The long-term effectiveness of atherectomy treatment for peripheral arterial disease is unknown. We studied 5-year clinical outcomes by endovascular treatment type among patients with peripheral arterial disease. Methods and Results We queried the Medicare-linked VQI (Vascular Quality Initiative) registry for endovascular interventions from 2010 to 2015. The exposure was treatment type: atherectomy (with or without percutaneous transluminal angioplasty [ PTA] ), stent (with or without PTA ), or PTA alone. The outcomes were major amputation, any amputation, and major adverse limb event (major amputation or any reintervention). We used the center-specific proportions of atherectomy procedures performed in the 12 months before a patient's procedure as the instruments to perform an instrumental-variable Cox model analysis. Among 16 838 eligible patients (median follow-up: 1.3-1.5 years), 11% underwent atherectomy, 40% received PTA alone, and 49% underwent stenting. Patients receiving atherectomy commonly underwent femoropopliteal artery treatment (atherectomy: 65%; PTA : 49%; stenting: 43%; P<0.001) and had worse disease severity (Trans-Atlantic Inter-Society Consensus score [TASC] B and greater; atherectomy: 77%; PTA : 68%; stenting: 67%; P<0.001). The 5-year rate of major adverse limb events was 38% in patients receiving atherectomy versus 33% for PTA and 32% for stenting (log rank P<0.001). Controlling for unmeasured confounding using instrumental-variable analysis, patients treated with atherectomy experienced outcomes similar to those of patients treated with PTA , except for a higher risk of any amputation (hazard ratio: 1.51; 95% CI , 1.08-2.13). However, compared with stenting, atherectomy patients had a higher risk of major amputation (hazard ratio: 3.66; 95% CI , 1.72-7.81), any amputation (hazard ratio: 2.73; 95% CI , 1.60-4.76), and major adverse limb event (hazard ratio: 1.61; 95% CI , 1.10-2.38). Conclusions Atherectomy is used to treat severe femoropopliteal and tibial peripheral arterial disease even though long-term adverse outcomes occur more frequently after this treatment modality.