Ommaya published over 150 articles, chapters, and books. His research focused on cancer treatment, traumatic brain injury, a CSF artificial organ, and philosophy of mind. Through discussions with Congressman William Lehman Chair of the House Appropriations Committee responsible for the Department of Transportation, he developed CDC's National Center for Injury Prevention and Control, which as part of its mission focuses on traumatic brain injury. As part of this effort Ommaya commissioned the IOM report Injury in America. The report called for the creation of the CDC center.
