Unmethylated cytosine-phosphate-guanine (CpG) motifs are often found in bacteria and viruses, but are rare in mammals. In mammals, CpG oligodeoxynucleotides (CpG ODN) stimulate the innate immune system via toll-like receptor 9 (TLR9). However, TLR9 is absent in birds; instead, TLR21 serves as the receptor for CpG ODN. While CpG ODN induce behavioral and physiological changes in mammals, there is limited research on their effects on behavioral and physiological parameters in birds. The aim of the present study was to determine whether intraperitoneal injection of K3, a synthetic class B CpG ODN, affected food intake, voluntary activity, cloacal temperature, blood constituents, and feed passage from the crop in chicks (
Gallus gallus
). Additionally, the effects of K3 (GC), which contains GpC motifs instead of CpG motifs, were investigated to determine the importance of these CpG motifs. Intraperitoneal injection of K3 significantly increased the mRNA expression of interleukin-1β, interleukin-6, interleukin-8, and interferon-γ in the spleen. These changes were not observed with K3 (GC) administration. Intraperitoneal injection of K3 significantly decreased food intake but did not affect voluntary activity. K3 also significantly increased cloacal temperature, tended to increase plasma glucose and corticosterone concentrations and significantly decreased feed passage from the crop. In contrast, K3 (GC) showed no effects on these parameters. These results demonstrate that class B CpG ODN is associated with anorexia, hyperthermia, and reduced feed passage through the digestive tract in chicks during bacterial and viral infections.