Beneficial as well as pathogenic microorganisms, derived from external and maternal sources, can inhabit the gut of hatchlings. In an effort to optimize the enteric development of chicks and to assist in the establishment of intestinal bacteria populations that are conducive to their good health and for their subsequent protection against invading pathogens, the in ovo administration of various biologics has been explored in various laboratories. This chapter discusses the various biologics tested for their effects on the gut microbiome and examines competitive exclusion cultures, specifically identified probiotics, prebiotics, synbiotics and nutrients. The chapter also looks at the prospects for the commercial in ovo use of these biologics during transfer, and looks ahead to future research trends in this area.