Host-pathogen interaction leads to either immunity or infection depending on the hosts susceptibility, virulence factors of the pathogen, route of entry, mode of pathogen transmission, and many environmental factors. A recent survey of human pathogens listed >1,400 different species; more than half are known to be zoonotic, of which at least 12% of all human pathogens are considered Emerging Infectious Diseases (EID). Influenza virus A, HIV/AIDS, SARS, MERS, Anthrax, Malaria and other arthropod-borne diseases are a few of them. EIDs continuously threaten all persons, regardless of age, sex, lifestyle, ethnic background, and socioeconomic status. We expect that understanding the mechanism of molecular components involved in host-pathogen interaction during infection with EIDs will provide a better opportunity to develop more efficacious control measures against them.