The invention relates to a system of automatic vaccination of eggs, developed for the purpose of vaccinating large quantities of fertile eggs in order to reduce the costs and labor involved, reduce embryonic mortality by increasing protection from diseases and reduce the stress in the first day of life of poultry chicks by eliminating the process of manually vaccinating each chick. The invention comprises an automatic system controlled by a PLC (programmable logic controller), using an injector that has a cylindrical body and cap made from high density non-corrosive plastic and together they form a pneumatic chamber, the cap containing an electronic contact sensor to signal empty egg spaces and avoiding wasting vaccine. The injector's pneumatic chamber contains a plasticized fiber sleeve to permit smooth movement of the pneumatic plunger. A needle passes through the plunger and a double acting spring in addition to securing the plunger in its starting position and returning it to the original position after the injection of vaccine, reduces the pressure on the needle after it breaks the egg shell to avoid harming the embryo. The injection platform that has conical holes for the injectors to permit lateral movements that allows the injectors to accommodate eggs that are tilted, with the injectors locked into position by a series of air bladders located within the platform and running parallel to the injectors. The sanitization system which disinfects the needle and the part of the injector in contact with the egg after every single injection is coupled with the removal of the incubator trays from the vaccination area to economize on production time.