The molecular mechanism underlying in the onset and maintenance of incubation behavior are not fully understood, and it is still unknown the reason why White Leghorn, a layer strain, hens never display incubation behavior. Therefore, to explore specific hypothalamic genes regulating incubation behavior, cap analysis of gene expression (CAGE) were applied to comparison between incubating Silkie and laying White Leghorn hens. In addition, mRNA expression of some differentially expressed genes (DEGs) and melanocortinergic appetite genes including agouti-related peptide (AgRP) and pro-opiomelanocortin (POMC) was also analyzed on Silkie hens under natural anorexia and starvation. The CAGE identified 217 hypothalamic DEGs in incubating Silkie hens, and that of two, transthyretin (TTR) and prolactin-releasing peptide (PrRP), suggested as appetite gene, were markedly up- and down-regulated in incubating hens, respectively. In addition, AgRP and POMC expression also increased in incubating bird. mRNA expression of TTR, PrRP, and appetite genes were not differed significantly by starvation, although TTR mRNA expression was relatively high in fasting hens. Consequently, transcriptome by CAGE identified a number of hypothalamic genes differentially expressed by incubation behavior in Silkie hens. Of these, it is suggested that TTR and PrRP may, at least in part, be related to adaptation to natural anorexia in incubating Silkie chickens.