Abstract The in vivo immunoadjuvant effects of CpG oligodeoxynucleotides (CpG-ODN) have been studied extensively in mice and relatively fewer studies have been done in piglets. But so far, the innate immunostimulatory effects of CpG-ODN combination with innate defense-regulator peptides (IDRs) have not been demonstrated. The purpose of this study is to determine the potential effects of CpG-ODN with IDR in newborn piglets. The immunostimulatory abilities of four selected IDRs were compared, among them HH2 showed best immunostimulatory effects in newborn piglets. Hereafter, the abilities of CpG-ODN combined with HH2 to enhance innate immune responses were examined in newborn piglets. The complex of HH2 and CpG-ODN could induce much stronger Th1 cytokine and chemokine responses than HH2 or CpG-ODN alone. HH2-CpG-ODN immunized piglets showed higher B cell percentage in PBMCs than CpG-ODN alone. These in vivo data demonstrated for the first time that subcutaneously (SC) administration of CpG-ODN combined with HH2 is efficient to stimulate innate immune system in newborn piglets.