The aim of this study was to evaluate the incidence, predictors, and long-term outcomes of patients with in-stent restenosis (ISR) after percutaneous coronary intervention (PCI) with drug-eluting stents (DES) for unprotected left main coronary artery (LMCA) disease. Few data on the clinical course and management of patients experiencing restenosis after DES treatment for unprotected LMCA disease have appeared. Between February 2003 and November 2007, 509 consecutive patients with unprotected LMCA disease underwent DES implantation, with 402 (80.1%) undergoing routine surveillance or clinically driven angiographic follow-up. A major adverse cardiac event was defined as the composite of death, myocardial infarction (MI), or target-lesion revascularization. The overall incidence of angiographic ISR in LMCA lesions was 17.6% (71 of 402 patients, 57 with focal-type and 14 with diffuse-type ISR. Forty patients (56.3%) underwent repeated PCI, 10 (14.1%) underwent bypass surgery, and 21 (29.6%) were treated medically. During long-term follow-up (a median of 31.7 months), there were no deaths, 1 (2.2%) MI, and 6 (9.5%) repeated target-lesion revascularization cases. The incidence of major adverse cardiac event was 14.4% in the medical group, 13.6% in the repeated PCI group, and 10.0% in the bypass surgery group (p = 0.91). Multivariate analysis showed that the occurrence of DES-ISR did not affect the risk of death or MI. The incidence of ISR was 17.7% after DES stenting for LMCA. The long-term clinical prognosis of patients with DES-ISR associated with LMCA stenting might be benign, given that these patients were optimally treated with the clinical judgment of the treating physician.