To establish the value of the SYNTAX Score-II (SS-II) in predicting long-term mortality of patients treated with left main PCI (LM-PCI) using second-generation drug-eluting stents (DES).The SYNTAX score (SS) and the SS-II were calculated in 804 patients included in the FAILS-2 registry (failure in left main study with 2nd generation stents). Patients were classified in low (SS-II ≤33; n = 278, 34.6%), intermediate (SS-II 34-43; n = 260, 32.3%) and high (SS-II ≥44; n = 266, 33.1%) SS-II tertiles. Primary endpoint was all-cause mortality. A significant difference in long-term mortality was noted (5.2 ± 3.6 years): 4.1, 7.5, and 16.7% in low, mid and high SS-II tertiles respectively (p < .001). SS-II score was more accurate in predicting mortality than SS (AUC = 0.73; 95%CI: 0.67-0.79 vs. AUC = 0.55; 95%CI: 0.48-0.63, respectively; p < .001). SS-II led to a reclassification in the risk of all-cause mortality re-allocating 73% of patients from the CABG-only indication to PCI or equipoise PCI-or-CABG indication. Using multiple Cox regression analysis, SS-II (HR: 1.07; 95%CI: 1.05-1.09; p < .001), along with Acute coronary syndrome (ACS) (HR: 1.66; 95%CI: 1.03-2.66; p = .07) and Cardiogenic shock (CS) (HR: 2.82 (95%CI: 1.41-5.64; p = .003) were independent predictors of long-term mortality. SS-II (HR: 1.05; 95%CI: 1.04-1.06; p < .001) along with Insulin dependent Type 2 DM (HR: 1.58, 95%CI: 1.09-2.30.; p < .05), ACS (HR: 1.58, 95%CI: 1.16-2.14; p < .001) and CS (HR: 2.02 95%CI 1.16-3.53; p < .05), were independent predictors of long-term MACE.The SS-II was superior to the SS in predicting outcomes associated with contemporary LM-PCI. In this real-world population, two clinical variables not included in the SS-II, ACS and T2DM, were identified as additional markers of poor outcome.