The evolution of the human brain has resulted in numerous specialized features including higher cognitive processes, such as language. The combination of our newfound communication expertise together with the process of transgenerational evolution at the epigenetic level has led to an exponential increase in human knowledge and abilities. In balance with these beneficent attainments though, the human brain has also acquired vulnerabilities to neuropsychiatric and neurodegenerative diseases, which reflect genetic and environmental factors. To understand the mechanisms of this disease susceptibility, a deeper appreciation of the developmental processes and their relationship to underlying features of brain evolution will be necessary. Knowledge of whole genome sequence and structural variation via high throughput sequencing technology provides an unprecedented opportunity to view human evolution at high resolution. However, phenotype discovery is a critical component of these endeavors and the use of non-traditional model organisms will also be critical for piecing together a complete picture. Ultimately, the union of developmental studies of the brain with studies of unique phenotypes in a myriad of species will result in a more thorough model of the groundwork the human brain built upon. Furthermore, these integrative approaches should provide important insights into human diseases.