In conclusion, we applied PPAR bioluminescent imaging-guided transcriptomic analysis to evaluate the organs that chitosan acted on and to analyze the molecular mechanisms of chitosan in this study. We found that administration of chitosan induced the PPAR-driven bioluminescent signals in brain and stomach. Microarray analysis showed that several pathways associated with lipid and glucose metabolism were regulated by chitosan. Moreover, we newly identified that chitosan may exhibit hypocholestemic and anti-obestic effects via downregulated expression of apoB and ghrelin genes. These findings suggested the feasibility of PPAR bioluminescent imaging-guided transcriptomic analysis on the evaluation of chitosan-affected metabolic responses in vivo. Moreover, we newly identified that downregulated expression of apoB and ghrelin genes were the novel mechanisms for chitosan-affected metabolic responses in vivo.