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 |
