The Estonian Doctoral School has six specialised sections, offering learning opportunities and support relevant to the field.
| Sections of the Doctoral School | Lead Partner | Partners |
| Mathematics, Computer Science and Informatics | Tallinn University of Technology | University of Tartu Tallinn University |
| Natural and Agricultural Sciences | University of Tartu | Tallinn University Tallinn University of Technology Estonian University of Life Science |
| Engineering and Technology | Tallinn University of Technology | University of Tartu Estonian Academy of Arts Estonian University of Life Science |
| Medical and Health Sciences, Veterinary Medicine | University of Tartu | Tallinn University Tallinn University of Technology Estonian University of Life Science |
| Social Sciences | University of Tartu | Tallinn University Tallinn University of Technology Estonian Business School |
| Humanities and Arts | Tallinn University | University of Tartu Estonian Academy of Arts Estonian Academy of Music and Theatre |
