Following entry into host via mucosal portal pathogen counter primary host defence through physical barrier and first line of defence via innate immune response. To counter these impediments, pathogens uses wide range of strategies that enable them to adhere and invade the gut epithelium followed by the induction of host inflammatory response. Specifically, host pathogen interaction at the mucosal surface leading to either immunity or infection is a multi-factorial process and depends on the susceptibility of the host, repertoire of virulence factors, mode of pathogen entry and transmission as well as many environmental factors. Depending on the nature of the pathogen, effective host response at the mucosal surface can be achieved by directing memory and effector immune cells to the mucosal membranes through tissue-specific homing receptors. Therefore, understanding the contributions of the individual host cell types and molecules towards infection or immunity provide stronger basis for developing efficacious control measures against emerging mucosal pathogen. In the past decade, the successful development of mucosal vaccines against many enteric and respiratory pathogens has boosted our interest in the field of mucosal immunity. With this background, we are currently studying the role of virulence repertories of emerging mucosal pathogens such as Influenza virus and Campylobacter jejuni in effective host response and exploring their potential as future vaccine candidate.