A number of crested chicken strains, such as the Polish chicken, exhibit a bony protuberance in the anterodorsal region of their skulls. The shape of their brain shows the anatomical peculiarity that is characterized by the upthrusting of cerebral hemispheres, called “cerebral hernia.” Some early works suggested that this phenotype may be caused by a genetic factor and any modifiers influencing the development of brain and/or skull. However, the causative gene and its formation mechanism are still unclear. The present study is aimed to analyze the inheritance and ontogenic process of cerebral hernia in the crested Polish chicken. Firstly, we constructed the resource family with the Polish chicken and PNP inbred strain. Genetic analysis of this family revealed that cerebral hernia is controlled by a single autosomal recessive gene and is closely associated with crest formation. Furthermore, our morphological analysis of brain structures in the progenies suggested that the significant enlargement of brain cavity at later stages of embryos, particularly after 15 days of incubation, may be the main cause of cerebral hernia. J. Exp. Zool. (Mol. Dev. Evol.) 9999B:613–620, 2012. © 2012 Wiley Periodicals, Inc.