Background The risk factors and long-term clinical outcomes of patients with definite stent thrombosis (ST) after second-generation drug-eluting stent (DES) implantation have not yet been adequately assessed. Methods and Results The REAL-ST (Retrospective Multicenter Registry of ST After First- and Second-Generation DES Implantation) included 313 definite ST of second-generation DES (early ST, n=179; late ST, n=66; very late ST, n=68). Four patients without definite ST of second-generation DES were identified as control patients for each ST case. Risk factors of definite ST were mostly different according to the timing of ST: ST-segment-elevation myocardial infarction, non-ST-segment-elevation myocardial infarction, and unstable angina at presentation, current smoking, left ventricular ejection fraction <40%, prior percutaneous coronary intervention, stent overlap, severely calcified lesion, left main coronary artery lesion, proximal left anterior descending lesion, postdiameter stenosis ≥20%, for early ST; age <70 years, ST-segment-elevation myocardial infarction at presentation, hemodialysis, left ventricular ejection fraction <40%, in-stent restenosis, and severely calcified lesion for late ST; and proximal left anterior descending lesion and in-stent restenosis for very late ST. Cumulative 4-year incidence of death after the index ST events was significantly higher in the ST patients than control patients (33.0% versus 12.3%, P<0.001 for early ST versus control; 30.6% versus 14.2%, P<0.001 for late ST versus control; and 28.0% versus 13.0%, P<0.001 for very late ST versus control, respectively). Conclusions Risk factors of definite ST after second-generation DES implantation were mostly different according to the timing of ST. Definite ST patients showed unfavorable long-term clinical outcomes compared with those without definite ST. Clinical Trial Registration URL: https://www.umin.ac.jp . Unique identifier: UMIN000025181.