Somatic deoxyribonucleic acid (DNA) damage has been associated with early-phase and/or acute complications of atherosclerosis. However, it remains unclear whether circulating levels of DNA damage have prognostic value in patients with coronary artery disease (CAD). The aim of this study was to assess the prognostic significance of chromosomal DNA damage in human lymphocytes on the rate of major adverse cardiovascular events in patients with CAD. A follow-up prospective cohort study was carried out of 178 patients (153 men, mean age 61.9 ± 9.7 years) with angiographically proved CAD who underwent micronucleus assay, a sensitive biomarker of chromosomal damage and genetic instability, from March 1999 and June 2001. During a mean follow-up period of 51.4 ± 23.8 months, 58 patients had major adverse cardiovascular events (cardiac death, myocardial infarction, stroke, congestive heart failure, unstable angina, or coronary and peripheral revascularization). The overall event-free survival rates were 77.5%, 70.4%, and 49.0% in patients in the lower, middle, and upper tertiles of micronucleus level, respectively (log rank = 11.5, p = 0.003). In a multivariate Cox regression model, only the upper tertiles were significantly associated with a higher risk for major adverse cardiovascular events (hazard ratio 2.2, 95% confidence interval 1.1 to 4.7, p = 0.03). In conclusion, levels of peripheral chromosomal DNA damage may be a new sensitive biomarker of prognostic stratification in patients with known CAD.