The SYNTAX score stratifies risk among drug-eluting stent-treated patients and is based on lesion characteristics alone. The Clinical SYNTAX Score (CSS) combines the SYNTAX score with age, ejection fraction, and creatinine clearance. We assessed its ability to stratify long-term outcomes in sirolimus-eluting stents (SES)-treated patients. Between August 2004 and March 2005, 249 patients were treated with SES. Clinical follow-up was evaluated at more than 5 years. The CSS was available for 206 patients. More than 5-year clinical follow-up data (mean 2114 ± 107 days) and CSS (range 1-322, mean 35.3 ± 49.9, median 17.5) were available for 201 patients. We divided these scores into tertiles: CSS-LOW ≤ 9.5, 9.5 < CSS-MID ≤ 28, and CSS-HIGH > 28. CSS-HIGH was associated with a higher death rate (CSS-LOW 9.0 %, CSS-MID 11.9 %, CSS-HIGH 41.8 %; log-rank p < 0.001) and major adverse cardiovascular events (MACE) (CSS-LOW 29.8 %, CSS-MID 35.8 %, CSS-HIGH 61.2 %; log-rank p = 0.004). Independent predictors for death were hemodialysis [hazard ratio (HR) 3.82; p < 0.001], age (HR 1.67; p = 0.003), ejection fraction (HR 0.98, p = 0.012) and CSS (HR 1.73, p = 0.028), and those for MACE were hemodialysis (HR 2.53, p = 0.002) and CSS (HR 1.40, p = 0.028). Areas under the curve for the SYNTAX score and CSS for death were 0.60 and 0.78 (p < 0.001), whereas those for MACE were 0.58 and 0.68 (p < 0.001), respectively. The CSS predicts long-term outcomes among SES-treated patients better than the SYNTAX score.