Selenium (Se) plays an important role in the brain development, function, and degeneration, nutritional encephalomalacia is closely related with dietary Se in avian. However, there is little evidence on the relationship between inflammation and encephalomalacia in avian and the mechanism which Se regulates the inflammatory response in brain tissues remains to be unclear. The present paper describes the effects of Se-deficient granulated diet on one transcription factor-nuclear factor kappaB and four pro-inflammatory cytokines-tumor necrosis factor, cyclooxygenase2, inducible nitric oxide synthase and Prostaglandin E synthase mRNA expression in the chicken brain tissues associated encephalomalacia. One hundred male chickens (1 day old; Weiwei Co. Ltd., Harbin, China) were divided into two groups (50 chickens per group). The expression levels in the brain tissues (cerebral gray matter, cerebral white matter, marrowbrain, cerebellum, thalamus and brain stem) were determined by real-time PCR on days 15, 25, 35, 45, and 55, respectively. The results showed the productions of pro-inflammatory mediators were increased following Se-deficiency. These data indicate the correlations between nutritional encephalomalacia and inflammatory response and the activity of inflammatory response in chicken brain may be induced by Se-deficiency.