Adipose tissue is the primary source of the adipokines resistin and fasting-induced adipose factor (FIAF). We reported that the brain is also a site of adipokine expression, although their function there is unknown. Peripheral resistin and fasting-induced adipose factor are reported to be inflammatory markers, and we hypothesized that they would be induced in the brain by hypoxia/ischaemia. We show that neonatal hypoxia/ischaemia rapidly increased fiaf mRNA in the injured cortex and hippocampus at 2 and 7 days after hypoxia/ischaemia. In contrast, resistin (retn) mRNA was increased in the cortex only at 21 days after hypoxia/ischaemia. As a lipopolysaccharide-induced inflammatory response did not increase brain fiaf and retn mRNA levels, we conclude that brain injury may be responsible for the novel hypoxia/ischaemia-induced changes in adipokine gene expression. In summary, our results indicate that brain injury, or an inflammatory stimulus, regulates the central expression of two genes normally considered to be adipose tissue-specific. These observations add to our previous evidence that the brain is an important site of adipokine gene expression.