Understanding of intraluminal structure and distribution of uncovered struts after drug-eluting stent implantation are limited by only 2-dimensional (2D) optical coherence tomography (OCT) images. We compared tissue coverage with 3-dimensional (3D) OCT and 2D quantitative analyses, and changes in intraluminal structure immediately after (baseline) everolimus-eluting stent (EES) implantation and at follow-up. The 2D analyses of uncovered struts ratio and tissue coverage thickness at a 0.5-mm interval were compared to 3D-OCT images and visually classified for the degree of tissue coverage. The difference in tissue coverage at baseline and follow-up after EES implantation was evaluated with tissue coverage scores (TCS) calculated by the 3D-OCT classification (Grade 0-3). 3D-OCT classifications were negatively correlated with uncovered-to-total struts (r = -0.864, P < 0.001) and positively correlated with tissue coverage thickness (r = 0.905, P < 0.001). Follow-up TCS was greater than baseline TCS (0.2 ± 0.4 vs. 1.4 ± 0.5, P < 0.001). Moreover, changes in intraluminal structures and longitudinal distribution of uncovered struts were assessed. Incomplete stent appositions, in-stent dissections, and thrombi were decreased at follow-up, indicating progressive arterial healing. The distribution of uncovered-to-total struts could be assessed by 3D-OCT, which was related to 2D analysis. Significant correlations between 3D-OCT classifications and quantitative analyses were shown. The classification and visual assessment of intraluminal structures by 3D-OCT were useful in evaluating arterial healing after EES implantation.