Background: Vaccines undoubtedly represent a promising and much needed approach to combatting infectious diseases, but there is also increasing evidence that they exert nonspecific effects, and these effects may be beneficial but also sometimes detrimental. Thus, here we sought to explore the effect of intranasal vaccination on the functions of pulmonary alveolar macrophages and neutrophils in calves of different ages.Results: Respiratory clinical signs and impaired microbicidal and phagocytic activities were observed for the alveolar neutrophils and vacuolized macrophages in the vaccinated calves compared with those in the unvaccinated calves, particularly at 15 days of age.Conclusions: Our results indicated that the use of some polyvalent attenuated and modified live virus vaccines in early stage of calves’ life, especially those under 15 days of age, should be restricted to farms in which the cattle are at a higher risk of contracting these viral infections, particularly considering the importance of alveolar macrophages and neutrophils against bacterial pathogens in a period of intense pulmonary challenge.