Background: The complexity of coronary artery disease (CAD) is a predictor of cardiovascular events in patients with >50 % diameter stenosis as determined by SYNTAX score. Here, we compare the Gensini score to SYNTAX in patients with CAD as well as apply the Gensini score in patients with nonobstructive CAD (NOB-CAD), defined by ≤50 % diameter stenosis, were the SYNTAX score cannot be utilized to define future risk. Methods: The AtheroGene study enrolled 2316 patients [861/37.2 % with acute cardiovascular syndrome (ACS) and 1500/62.8 % with stable CAD (SCAD)]. Of these, 1966 had obstructive CAD (OB-CAD) with SYNTAX and Gensini scores available and 291 events with either cardiovascular mortality or non-fatal myocardial infarction were recorded. Furthermore, 350 patients had NOB-CAD with only Gensini score and 36 events. Median follow-up time was 4.9 years. Results: In the OB-CAD cohort the SYNTAX and the Gensini score predicted outcome. Kaplan–Meier curve analysis with the dichotomized Gensini score showed a significant result (p = 0.04) in the NOB-CAD cohort. Cox Regression analysis after adjustment showed a hazard ratio (HR) of 1.33 and p = 0.04 for the Gensini score in the NOB-CAD cohort. Receiver operating characteristic curve (ROC) analysis provided the highest area under the curve (AUC) regarding the outcome for the Gensini score with 0.65 (p = 0.004). Comparing the SYNTAX and Gensini score in this cohort showed improved discrimination of patients with events by the Gensini score (p = 0.02). Conclusion: The Gensini score predicted events in patients with ≤50 % diameter lesions. Utilization of this score is useful to define risk in NOB-CAD patients.