Genetic studies in animal models have started to open new ways for understanding the underlying molecular pathophysiology of hydrocephalus. Human hydrocephalus can be classified as syndromic versus non-syndromic, and congenital versus acquired. Comparative twin studies have been performed to analyze the genetic influences in congenital structural defects including hydrocephalus. Familial hydrocephalus has long been suggested as a heritable disease, with heterogeneous causes, which may result from distinct monogenic or multifactorial disorders. Congenital hydrocephalus (CHC) is usually the consequence of deficient brain development and perturbed cellular function, implicating the important roles that CHC genes play during brain development. The majority of identified hydrocephalus loci and genes are from genetic analysis in hydrocephalic animal models. The pathophysiology of hydrocephalus in the ventricular system has been extensively studied through either down- or up-regulation of certain targeted gene expression, followed by comparative morphological and molecular studies.