Vaccination is a common routine for prevention and control of human and animal diseases by inducing antibody responses and cell-mediated immunity in the body. Through vaccinations, smallpox and some other diseases have been eradicated in the past few years. The use of a patho- gen itself or a subunit domain of a protein antigen as immunogens lays the basis for traditional vaccine development. But there are more and more newly emerged pathogens which have expe- rienced antigenic drift or shift under antibody selective pressures, rendering vaccine-induced im- munity ineffective. In addition, vaccine development has been hampered due to problems includ- ing difficulties in isolation and culture of certain pathogens and the antibody-dependent enhancement of viral infection (ADE). How to induce strong antibody responses, especially neu- tralizing antibody responses, and robust cell-mediated immune responses is tricky. Here we re- view the progress in vaccine development from traditional vaccine design to reverse vaccinology and structural vaccinology and present with some helpful perspectives on developing novel vac- cines.