HIV, Influenza virus and Neisseria meningitidis B continue to pose a severe threat worldwide, causing thousands of deaths and an enormous economic loss every year. The major problem in fighting with these infectious diseases is high genetic variability and rapid formation of variants that escape the acquired immunity against previous strains, or have resistance to antimicrobial agents. Therefore, development of an alternative antimicrobial strategy that can be applicable to any new strain without prior prediction is the high priority in pharmaceutical industry. The administration of vaccines is called vaccination. Vaccination is the most effective method to prevent and eradicate infectious diseases. Limitations to their effectiveness, nevertheless, exist. New trends in vaccine development could prevent vaccine resistance and improve efficiency.