Objectives. The purpose of this study was to analyze the success rates for excimer laser-assisted coronary angioplasty performed in patients undergoing angioplasty for lesions containing thrombus. Background. The presence of intracoronary thrombus increases the risk of a poor clinical outcome after balloon angioplasty. The effect of intracoronary thrombus on the safety and efficacy of excimer laser-assisted coronary angioplasty is unknown. Methods. Percutaneous excimer laser-assisted coronary angioplasty was attempted in 142 patients, of whom 12 had angiographic evidence of intracoronary thrombus in 14 lesions, defined as a filling defect surrounded by contrast medium or an area of contrast staining. Results. Clinical success (<50% residual stenosis without myocardial infarction, death or bypass surgery at any time during hospitalization) was achieved in 7 (58%) of the 12 patients with intracoronary thrombus, compared with 123 (95%) of the 130 patients without thrombus (p = 0.00001). Angiographic and clinical complications were more common in patients with thrombus: embolization (25 % vs. 1 %, p < 0.001), myocardial infarction (33% vs. 2%, p < 0.001), abrupt closure (17% vs. 4%, p = 0.049). Angiographic restenosis at 6 months was seen at 7 (70%) of 10 treated sites with intracoronary thrombus and at 59 (51%) of 116 sites without thrombus (p = 0.245). Presence of intracoronary thrombus was identified as the most important predictor of clinical success (p = 0.013) by multivariable logistic regression analysis, which controlled for other covariables, such as lesion complexity or lesion location in a saphenous vein graft. Conclusions. This analysis shows that the success of excimer laser-assisted coronary angioplasty is compromised when thrombus is detected angiographically. Further investigation of other strategies is needed to improve the outcome of angioplasty for this challenging problem.