In order to understand the chitosan-induced biological events in brain and stomach, we extracted RNA samples from brain and stomach on 3 d and performed microarray analysis. In a total of 29,922 genes, the transcripts of 154 and 143 genes in the stomach and brain, respectively, passed the aforementioned criteria (Table S1 and Table S2) and selected for KEGG classification. Tables 1 and 2 show the pathways significantly regulated by chitosan in the stomach and brain, respectively. Five pathways, including oxidative phosphorylation, ribosome, GnRH signaling pathway, tumor necrosis factor-α (TNF-α) signaling pathway and insulin signaling pathway, were affected commonly by chitosan in both organs, and oxidative phosphorylation and ribosome pathways were the top two pathways affected by chitosan. The majority of pathways, including oxidative phosphorylation, pyruvate metabolism, GnRH signaling pathway, glycolysis/gluconeogenesis, benzoate degradation, glycerolipid metabolism, ether lipid metabolism, glutathione metabolism, insulin signaling pathway, alanine and aspartate metabolism and IGF signaling pathway, were associated with lipid and glucose metabolism. These data showed that chitosan might alter several pathways involved in lipid and glucose metabolism in brain and stomach.