Vaccination programs aim to prevent the target infectious disease and also prevent complications and mortality related to this disease. However, with the widespread use of vaccines, the number of individuals with the potential to infect the pathogen in the community decreases, so that the contact of the non-vaccinated individuals with the pathogen decreases, and these individuals are protected indirectly. In addition, vaccines have secondary positive effects on overall morbidity and mortality rates in the community, which cannot be explained by the prevention of target disease. Secondary effects due to vaccine applications have attracted more attention from researchers in recent years. Accurate, clear, and standard observation methods should be applied to identify secondary effects on vaccine applications. Epidemiological surveillance should be carried out carefully to determine the burden of the disease, to reveal target groups and to determine the effect of immunization programs. In this way, it is possible to act with simple and evidence-based information when determining a national immunization program.