A 54 years old man underwent directional coronary atherectomy in segment 7 with a partial deep-cut injury. A sirolimus-eluting stent (SES) was implanted at the restenosed post-atherectomy lesion. Six months after SES implantation, intravascular ultrasound (IVUS) examination revealed slight vessel enlargement although there were no malapposed struts. Optical coherence tomography (OCT) revealed partial stent malapposition. Ticlopidine was discontinued 3 months after SES implantation, but aspirin was continued. Twenty-nine months after SES implantation, after discontinuing aspirin for 7 days for colon polypectomy, the patient suffered an acute myocardial infarction at the SES implantation site. IVUS revealed further positive vessel remodeling and slight stent malapposition and OCT revealed extension of the previous stent malapposition and ulcer-like appearance around the stent struts. This case demonstrates that even a small partial SES malapposition that can be detected only by OCT has the potential to enlarge over time and the late malapposition may result in late thrombosis when anti-platelet therapy is discontinued.