The association between incomplete revascularization (IR) and long-term mortality after stenting in the era of drug-eluting stents is not well understood. In the present study, we test the hypothesis that IR is associated with a greater risk of long-term (5-year) mortality after stenting for multivessel coronary disease. Using data from the Percutaneous Coronary Intervention Reporting System of New York State, 21,767 patients with multivessel disease who underwent stenting during October 2003 to December 2005 were identified. Complete revascularization (CR) was achieved in 6,844 patients (31.4%), and 14,923 patients (68.6%) were incompletely revascularized. The CR and IR patients were propensity matched on a 1:1 ratio on the number of diseased vessels, the presence of total occlusion, type of stents, and the probability of achieving CR estimated using a logistic model with established risk factors as independent variables. Patients were followed for vital status until December 31, 2008 using the National Death Index. Differences in survival between the matched CR and IR patients were compared. Among the 6,511 pairs of propensity-matched patients, the 5-year survival rate for IR was lower compared with CR (79.3% vs 81.4%, p = 0.004), and the risk of death during follow-up was 16% greater for IR compared with CR (hazard ratio 1.16, 95% confidence interval 1.06 to 1.27, p = 0.001). In addition, subgroup analyses demonstrated that the association between IR and long-term mortality was not dependent on major patient risk factors. In conclusion, IR is associated with an increased risk of long-term mortality after stenting for multivessel disease in the era of drug-eluting stents.