The gastric cancer is one of the most common carcinomas and the second cancer-related death in the world. The risk factors for this cancer include genetic factors and environmental factors such as Helicobacter pylori infection. The protein HcpD (HP0160) of H. pylori is a member of the cysteine-rich protein family that interacts with host immune systems. One of the modern approaches to stimulate the humoral and cellular immune systems against diseases is utilization of DNA vaccines. Using qPCR method, this study aimed to evaluate the expression level of cytokines genes including IL17, IL4, and interferon gamma (IFNγ) in BALB/c mice vaccinated with pCDNA3.1(–)-hcpD DNA vaccine against H. pylori. In this study, pCDNA3.1(–)-hcpD recombinant vector was prepared and transformed into E. coli to obtain a large number of plasmids. After plasmid purification and confirmation of the transformation by digestion and PCR, the chitosan nanoparticles were synthesized using ionic gelation method. The injectable solutions containing pCDNA3.1(–)-hcpD, pCDNA3.1(–)-hcpD + nanoparticles or pCDNA3.1 (empty vector as control group) were injected into BALB/c mice, separately. Then, the blood and tissues samples from each animal were collected and the expression levels of cytokine genes were examined by a qRT-PCR method. The IL-4 expression level was significantly decreased in pcDNA3.1(–)-hcpD + nanoparticle and pcDNA3.1(–)-hcpD groups (p < 0.001). Conversely, the expression level of IFNγ gene in both groups was increased significantly (p < 0.001). The expression level of IL17 gene showed no significant difference between DNA vaccine containing nanoparticle compare with pcDNA3.1(–)-hcpD (p > 0.05). During 15, 30 and 45 post-injection days, the expression level of hcpD decreased in hip tissue of mice vaccinated with pcDNA3.1(–)-hcpD and pcDNA3.1(–)-hcpD + nanoparticle although no significant difference found between the vaccinated groups (p > 0.05). pcDNA3.1(–)-hcpD vaccine can stimulate the immune system in vaccinated mice either as the sole agent or combined with chitosan nanoparticles. Therefore this method can be an effective way for immunization against H. pylori infection.