The synthetic unmethylated oligodeoxynucleotides with CpG motifs (CpG ODN) were shown to activate Toll-like receptor 21 (TLR21) and stimulate the innate and adaptive immune system. In this study we tested the expression of TLR21, interferon (IFN)-γ and interleukin (IL)-1β mRNA in the blood after subcutaneous and intraocular application of the class B CpG ODN in chicken. The relative expression of mRNA of TLR21, IFN-γ and IL-1β were quantified at 3, 6, 12, 24 and 72 h post-stimulation. The study revealed that IFN-γ mRNA expression was significantly upregulated 12 h after subcutaneous stimulation with a high and low dose of ODN CpG, whereas the IL-1β mRNA expression levels were significantly upregulated 3 and 72 h after subcutaneous administration. After intraocular administration, the IL-1β mRNA levels were the highest at 24 h post-application, albeit not specifically. This data indicates that class B CpG ODN has the ability to induce TLR21 response in blood when administered parenterally in chicken. In contrast, intraocular administration of CpG ODN was not able to produce a significant increase in cytokine mRNA expression in blood. The data suggest that additional stimulus, e.g. the antigen, may be needed on the site of mucosal administration to activate systemic immune response.