Yes. Without an identifiable pathogen (a disease-causing microorganism such as a bacterium or virus) there can be no vaccine. Vaccines are essentially based on, or derived from, weakened (attenuated) or dead (inactivated) germs. In some cases they are produced from other pathogens that are closely related to the disease-causing pathogen.
If scientists did not understand the pathogens themselves, the development of vaccines would not have been possible.
For more information, see ‘Vaccination – 20 Objections & Responses’, produced by the Robert Koch Institute and Paul Ehrlich Institute