Primary prevention of congenital anomalies was identified as an important action in the field of rare diseases by the European Commission in 2008, but it was not included in the Council Recommendation on an action in the field of rare diseases in 2009. However, primary prevention of congenital anomalies is feasible because scientific evidence points to several risk factors (e.g., obesity, infectious and toxic agents) and protective factors (e.g., folic acid supplementation and glycemic control in diabetic women). Evidence-based community actions targeting fertile women can be envisaged, such as risk-benefit evaluation protocols on therapies for chronic diseases, vaccination policies, regulations on workplace and environmental exposures as well as the empowerment of women in their lifestyle choices. A primary prevention plan can identify priority targets, exploit and integrate ongoing actions and optimize the use of resources, thus reducing the health burden for the new generation. The EUROCAT-EUROPLAN recommendations for the primary prevention of congenital anomalies endorsed in 2013 by the European Union Committee of Experts on Rare Diseases present an array of feasible and evidence-based measures from which national plans can adopt and implement actions based on country priorities. Primary prevention of congenital anomalies can be achieved here and now and should be an integral part of national plans on rare diseases.