The H-Tx rat is a polygenic inherited model of hydrocephalus. In order to identify disease-specific biomarkers associated with congenital hydrocephalus, comparative proteomic analysis was used to screen cerebellum proteins in H-Tx rats at 1 day after birth. Seven proteins showed significant changes in hydrocephalic H-Tx rats compared with Sprague-Dawley and normal H-Tx rats, including HMG-1, CDCrel-1A, mitochondrial ATP synthase, ERp29, NADP+-ICDH, CCT beta and gamma. This indicates that the hydro-cephalus in H-Tx rats may be the result of a panel of proteins. In particular, the presence of HMG-1 and lack of CDCrel-1 in hydrocephalic H-Tx rats suggests that the use of two protein markers will provide further insight with respect to congenital hydrocephalus.