Background Late incomplete stent apposition (ISA) may occur after drug-eluting stent implantation, affecting long-term clinical outcomes. This study aimed to evaluate the impact of clinical presentations of coronary artery disease on late ISA after percutaneous coronary intervention (PCI) with sirolimus-eluting stents (SES) by means of three-dimensional volumetric intravascular ultrasound (IVUS) analyses. Methods One hundred and thirty-seven patients with coronary artery disease received SES implantation during PCI and had repeat angiography with IVUS examination. All patients were followed up one year after the procedure. Results In overall 219 treated lesions (137 patients), late ISA was identified in 25 lesions (16 patients). Clinical diagnosis of acute coronary syndrome (ACS) and use of long stents were more common in patients with than in those without late ISA. Patients with late ISA had greater external elastic membrane (EEM) area in stented segment ((15.34+5.44) vs (13.83=,-4.51 ) mm2, P=0.026), stented-to-reference segment EEM area ratio (1.13±0.22 vs 1.02±0.18, P ＜0.001), and plaque and media area ((8.43±3.93) vs (7.01±2.93) mm2, P =0.002) than in those without late ISA. Multivariate Logistic regression analysis showed that clinical diagnosis of ACS and use of long stents were independent risk factors for late ISA (OR 6.477, 95%C/ 2.297-18.263, P＜0.001; OR 3.680, 95%C/ 1.181-11.469, P =0.025; respectively). During one-year follow-up after IVUS examination, the rate of very late stent thrombosis tended to be higher in patients with than in those without late ISA (18.7% vs 3.3%, P=0.051). Conclusions The occurrence of late ISA after SES implantation may be related to clinical status, use of long stents, and marked positive vessel remodeling. Late ISA tended to increase the rate of very late stent thrombosis during follow-up, highlighting the importance of long-term dual antiplatelet therapy for these patients.