Effective immunization of neonates is an important goal for vaccinology. We show that inoculation of newborn mice with a mixture of plasmids expressing influenza hemagglutinin (HA) and nucleoprotein (NP) genes leads to an enhanced protection subsequent to the lethal challenge with two distinct strains. In sharp contrast, neonatal injection with UV-inactivated influenza virus strain WSN, failed to induce protection against the homologous challenge. Our results show that while plasmid immunization of neonates elicits a protective immunity, the immunization with inactivated virus does not.