The SYNTAX score (SS) was recently introduced to overcome the limitation of coronary angiography in the interpretation of multivessel coronary artery disease (MVD). The SS is an angiography-based scoring system that describes lesion complexity and correlates with clinical outcomes. However, angiographic assessment of MVD often over- or underestimates the functional significance of MVD. A fractional flow reserve-guided SS, termed the functional SS (FSS), which is obtained by counting only ischemia-provoking lesions, can overcome this limitation. Compared with the classic SS, the FSS has better reproducibility and prognostic value, and it increases the proportion of patients with MVD who fall into the lowest risk for adverse events after percutaneous coronary intervention. Therefore, the selection of target vessels, the method for revascularization and the determination of prognosis in patients with MVD are improved by calculating the FSS in daily practice.