Many studies have demonstrated that late or very late thrombosis after drug-eluting stent (DES) implantation may be related with incomplete neointimal coverage. We investigated long-term (≥2 years) results of neointimal coverage following sirolimus-eluting stent (SES) and paclitaxel-eluting stent (PES) implantation using optical coherence tomography (OCT). A follow-up angiography with OCT examination was performed in 29 patients with 32 lesions for more than 2 years (group 1; 1,066 ± 381 days) and 101 patients with 104 lesions at 9 months (group 2; 273 ± 33 days) after the index procedure. The status of neointimal coverage and stent apposition was evaluated. The number of stents with completely covered struts was higher (25.0% in group 1 vs. 13.5% in group 2, P = 0.12). The percentage of uncovered struts (5.4 ± 7.5% in group 1 vs. 8.5 ± 11.6% in group 2, P = 0.19) and that of malapposed strut (0.5 ± 1.4% vs. 1.5 ± 4.2%, respectively, P = 0.19) were lower in group 1. While the percentage of uncovered and malapposed struts were quite similar in the PES groups between the two groups (P = 0.54 and 0.65, respectively), there were lower trends in the percentage of uncovered and malapposed struts in the SES group (P = 0.09 and 0.09, respectively). In conclusion, incomplete neointimal coverage was still observed in a majority of DESs and considerable struts were not covered with neointima even at more than 2 years after DES implantation. The pattern of neointimal coverage between 9-month and 2-year appeared to be somewhat different between PES and SES.