This qualitative research aims to examine the establishment and challenges of research universities in Turkey. To this end, specifying their missions, funding, leadership, autonomy, physical and academic infrastructures of research universities were researched. The data were collected through interviews and analyzed with content analysis technique. Research results revealed that as all research universities in Turkey were chosen among existing universities without making their missions clear, preparing their academic and physical infrastructures ready in advance, they face severe challenges regarding specifying their missions, leadership, funding, and autonomy, physical and academic infrastructure. Only a benefit of having considerably 25% more academic staff employment chance was noted in the study. It can be concluded that the idea of the establishment of research universities has no clear understanding, and due to insufficient planning, unclear policies, and legal base, they are bound to fail in the long term.