Background: Stent thrombosis (ST) following the implantation of drug-eluting stents (DES) remains the major limitation of this new technology. The identification of modifiable correlates of ST may help reduce this catastrophic event. Methods: This was a retrospective, single-center, lesion-based study. A cohort of 45 consecutive lesions (35 patients) initially treated with successful DES implantation from May 2003 to February 2005 that re-presented with ST within 12 months was identified. This cohort was compared to a control group of 1,620 unselected lesions (1,187 patients) that were successfully treated with DES implantation and which remained free of ST. Comparison of angiographic and procedural features was made between the ST and no-ST groups, and logistic regression analysis was then performed to identify independent correlates of ST. For the purposes of the study only definite ST events (angiographically or autopsy proven) were considered. Results: Independent angiographic predictors of cumulative ST at 12 months were left anterior descending (LAD) artery (OR: 1.91, CI: 1.01-3.59, P = 0.045), bifurcation (OR: 2.43, CI: 1.06-5.56, P = 0.035), and in-stent restenotic (OR: 2.64, CI: 1.12-6.25, P = 0.027) lesions. Procedural predictors were number of stents per lesion (OR: 2.30, CI: 1.29-4.11, P = 0.005) and intravascular ultrasound (IVUS) guidance (OR: 0.45, CI: 0.24-0.84, P = 0.013). Correlates of subacute events were LAD artery, proximal segment, and lack of IVUS guidance. Correlates of late ST were bifurcation and in-stent restenotic lesions. Conclusions: Angiographic and procedural correlates of subacute and late ST after DES implantation differ. Lack of IVUS guidance was the only modifiable predictor identified. Treatment of bifurcation and restenotic lesions was predictive of late events.