Although favorable clinical outcomes have been demonstrated for fluoropolymer-based paclitaxel-eluting stents (FP-DES) in the treatment of femoropopliteal lesions, the vascular response after implantation has not been systematically studied through intravascular imaging.Methods and Results: We angioscopically compared FP-DES: 24 in the early phase (mean [±SD] 3±1 months), 26 in the middle phase (12±3 months), and 20 in the late phase (≥18 months) after implantation. The dominant neointimal coverage grade, heterogeneity of neointimal coverage grade, and thrombus adhesion in the stent segment were evaluated. Neointimal coverage was graded as follows: Grade 0, stent struts exposed; Grade 1, struts bulging into the lumen, although covered; Grade 2, struts embedded in the neointima, but visible; Grade 3, struts fully embedded and invisible. Dominant neointimal coverage and heterogeneity grades were significantly higher in the middle and late phases than in the early phase (all P<0.05), but did not differ significantly between the middle and late phases. The incidence of thrombus adhesion was recorded for all stents in each of the 3 different phases. The middle and late phases after FP-DES implantation were associated with significantly higher dominant neointimal coverage and heterogeneity grades than the early phase. However, thrombus adhesion was observed in all phases after FP-DES implantation. Arterial healing may not be completed even in the late phase after FP-DES implantation.