Background: Although familial hypercholesterolemia (FH) confers a high risk of coronary artery disease, most patients are undiagnosed, and little is known about the efficiency of genetic cascade screening programs at national level. Objective: The aim of the study was to estimate the cost-effectiveness of a national genetic cascade screening program in Spain. Methods: An economic evaluation was performed using a decision tree analysis. The choice in the decision tree was between implementation of the national program for FH (NPFH) or keeping the usual clinical care. The NPFH detects FH patients through total cholesterol measurement at primary care level and use of genetic testing in index cases and relatives. The payer (National Health System) and social (including the productivity lost) perspectives were considered. The outcome variables were coronary events avoided, deaths avoided, and quality-adjusted life years (QALYs) gained. Results: From the payer perspective, the application of the NPFH during 1 year prevents 847 coronary events and 203 deaths in the 9000 FH patients cohort during a 10-year follow-up, yielding an extra 767 QALYs, at a cost of €29,608 per QALY gained. From the social perspective, the NPFH is dominant over the control (the cost decreases and the effectiveness increases). The sensitivity analysis confirms the robustness of the findings. Conclusion: The NPFH based on molecular testing is a cost-effective diagnostic and management strategy that supports government expenditure aimed at preventing coronary artery disease in FH patients in Spain. Implementation of such a strategy is likely to be also cost-effective in countries with similar developed healthcare systems.