EndoSysScore (ESS) v3.0 is a phenotype-aware stacking ensemble for predicting 30-day mortality after cardiac surgery for infective endocarditis, developed on the GIROC Italian multicenter registry (24 centres, 2010–2023; derivation cohort n=4,334) and evaluated in an independent external validation cohort of 881 patients from three centres. Performance (independent external validation, n=881, 3 centres):- AUC 0.789 (95% CI 0.751–0.827)- 6/6 DeLong superiority over all comparators (all p<0.05)- O/E ratio 0.994- Mean absolute deviation on rare phenotypes: 3.8 pp vs 9.4–38 pp for comparators Six high-risk phenotypes (A–F) identified in derivation data and validated externally. TIMA-3 blind realism test: 10 cardiac surgeons, 1,000 judgements, pooled accuracy 49.5% (p=0.776 vs chance). This is the updated version of the original deposit (doi:10.5281/zenodo.20327975, SYS Score v2.0). The model architecture has been updated from bagged XGBoost to a LightGBM meta-learner with phenotype-aware sample weighting. The validation cohort has been expanded from a single centre (n=597) to three independent centres (n=881). Live calculator: https://endosysscore.orgGitHub: https://github.com/sandro2462/sys-score