Omphalitis or yolk sac infection (YSI) and colibacillosis are the most common infectious diseases that lead to high rates of early chick mortalities (ECMs) in young chicks. Out of numerous microbial causes, avian pathogenic Escherichia coli (APEC) or extraintestinal pathogenic E. coli infections are considered the most common cause of these conditions. YSI causes deterioration and decomposition of yolk, leading to deficiency of necessary nutrients and maternal antibodies, retarded growth, poor carcass quality, and increased susceptibility to other infections, including omphalitis, colibacillosis, and respiratory tract infection. Presently, in ovo injection of antibiotics, heavy culling, or after hatch use of antibiotics is practiced to manage ECM. However, increased antibiotic resistance and emergence of “super bugs” associated with use or misuse of antibiotics in the animal industry have raised serious concerns. These concerns urgently require a focus on host-driven nonantibiotic approaches for stimulation of protective antimicrobial immunity. Using an experimental YSI model in newborn chicks, we evaluated the prophylactic potential of three in ovo–administered innate immune stimulants and immune adjuvants for protection from ECM due to YSI. Our data have shown >80%, 65%, and 60% survival with in ovo use of cytosine-phosphodiester-guanine (CpG) oligodeoxynucleotides (ODN), polyinosinic:polycytidylic acid, and polyphosphazene, respectively. In conclusion, data from these studies suggest that in ovo administration of CpG ODN may serve as a potential candidate for replacement of antibiotics for the prevention and control of ECM due to YSI in young chicks.