Several studies have shown coronary endothelial dysfunction and delayed arterial healing associated with first-generation drug-eluting stents. However, it remains unclear whether those issues persist for a longer term. We thus evaluated serial changes in endothelial function and intra-stent condition after paclitaxel-eluting stents (PES) implantation. Eight patients with stable effort angina were assessed at 9 and over 24 months (1st and 2nd follow-up) after PES implantation. Endothelial function was evaluated with intracoronary infusion of acetylcholine (Ach). Vascular responses were quantitatively measured. Intra-stent condition was evaluated using angioscopy. We assessed (1) the degree of neointimal coverage over the stent (grade 0: no coverage to grade 3: full coverage); (2) presence of yellow intima inside the stent, and (3) existence of in-stent thrombus. Vasomotions proximal to the stent at 2nd follow-up significantly improved compared with 1st follow-up (p = 0.04), whereas vascular responses at the distal segment did not differ between 1st and 2nd follow-up (p = 0.19). From the angioscopic study, the average of coverage grading was comparable between the 2 points (0.9 ± 0.8 vs. 1.3 ± 1.0, p = 0.20). In addition, the incidence of yellow intima and in-stent thrombus did not differ between 1st and 2nd follow-up (yellow intima; 50 vs. 37.5 %, p = 1.0, thrombus; 75 vs. 50 %, p = 0.61). Endothelial dysfunction and delayed healing with PES could attenuate gradually, but these issues may persist over 24 months in some patients.