Background The durable presence of polymer coating on drug-eluting stent (DES) surface may be one of the principal reasons for stent thrombosis. The long-term coronary arterial response to biodegradable polymer-coated sirolimus-eluting stent (BSES) in vivo remained unclear.Methods Forty-one patients were enrolled in this study and virtual histology intravascular ultrasound (VH-IVUS) was performed to assess the native artery vascular responses to BSES compared with durable polymer-coated SES (DSES) during long-term follow-up (median: 8 months). The incidence of necrotic core abutting to the lumen was evaluated at follow-up.Results With similar in-stent late luminal loss (0.15 mm (0.06-0.30 mm) vs. 0.19 mm (0.03-0.30 mm), P=0.772), the overall incidence of necrotic core abutting to the lumen was significantly less in BSES group than in DSES group (44% vs.63%, P ＜0.05) (proximal 18%, stented site 14% and distal 12% in BSES group, proximal 19%, stented site 28% and distal 16% in DSES group). The DSES-treated segments had a significant higher incidence of necrotic core abutting to the lumen through the stent struts (73% vs. 36%, P ＜0.01). In addition, more multiple necrotic core abutting to the lumen was observed in DSES group (overall: 63% vs. 36%, P ＜0.05). Furthermore, when the stented segments with necrotic core abutting to the lumen had been taken into account only, DSES-treated lesions tended to contain more multiple necrotic core abutting to the lumen through the stent struts than BSES-treated lesions (74% vs. 33%), although there was no statistically significant difference between them (P=0.06).Conclusions By VH-IVUS analysis at follow-up, a greater frequency of stable lesion morphometry was shown in lesions treated with BSESs compared with lesions treated with DSESs. The major reason was BSES produced less toxicity to the arterial wall and facilitated neointimal healing as a result of polymer coating on DES surface biodegraded as time went by.