Background: Emotional and behavioral problems in childhood often have far-reaching consequences for social, emotional and cognitive development, which is why their prevention is of great importance. However, preventive measures during childhood are rarely taken. Objectives: As part of a health care implementation study, it will be examined whether systematic screening, embedded in routine pediatric health check-ups promotes the identification of children at risk and the allocation to preventive programs. Methods: For this purpose, a screening via the Strengths and Difficulties Questionnaire is planned during the regular health check-ups (U9–U11) of approximately 3500 children aged 5–10 years in about 53 medical practices within a 20 km radius of Dresden (Germany). The parents receive feedback concerning the results from the pediatrician and, in case of borderline results on the subscales “emotional problems” and “behavioral problems”, a recommendation for an indicative prevention program. Children and parents will be assessed at four points in time with standardized and project-specific questionnaires. Furthermore, guided interviews with the health professional and the parents will be conducted. Results and conclusions: The feasibility, utility and acceptance of a screening for emotional and behavioral problems of children and recommendations for their prevention in pediatricians’ practices will be evaluated in a pre–post comparison and after 12 months. Beneficial and inhibiting factors for the utilization are to be identified and used to derive recommendations for the implementation of preventive measures in standard care, identify emotional and behavioral problems at an early stage and prevent the development of mental disorders.