Ostial right coronary artery (RCA) lesions are associated with a high restenosis rate after bare-metal stent implantation. However, long-term outcomes after drug-eluting stent (DES) implantation for ostial RCA lesions have not been adequately evaluated. Among 12824 patients enrolled in the j-Cypher registry, 5-year outcomes were compared between 397 patients with ostial RCA lesions, and 3716 patients with non-ostial RCA lesions treated with sirolimus-eluting stents (SES). Through 5-year follow-up, patients with ostial RCA lesions had a significantly higher cumulative incidence of target lesion revascularization (TLR) (28.2 versus 13.7 %, P < 0.0001) than those with non-ostial RCA lesions. After adjusting for confounders, excess TLR risk of the ostial group relative to the non-ostial group was significant for both early TLR within 1-year and late TLR beyond 1-year (HR 2.14 [95 % CI 1.59-2.84], P < 0.0001, and HR 1.58 [95 % CI 1.06-2.26], P = 0.02, respectively). Although the cumulative incidence of death was also significantly higher in the ostial group than in the non-ostial group (25.7 versus 14.4 %, P < 0.0001), the excess risk of the ostial group relative to the non-ostial group was no longer significant after adjusting for confounders (HR 1.25 [95 % CI 0.99-1.57], P = 0.07). SES implantation for ostial RCA lesions was associated with higher risk for TLR as compared with that for non-ostial RCA lesions. Restenosis, both early and late, remains an issue in coronary DES implantation for ostial RCA lesions.