| Programme | Mode | Length* | Degree | Faculty |
| Advanced Materials and Nanosciences (P3960) | combined | 4 | Ph.D. | PřF |
| Advanced Materials and Nanosciences (P3960) | full-time | 4 | Ph.D. | PřF |
| Anatomy, Histology and Embryology (4-years) (P5154) | combined | 4 | Ph.D. | LF |
| Anatomy, Histology and Embryology (4-years) (P5154) | full-time | 4 | Ph.D. | LF |
| Anesthesiology, Intensive Medicine and Pain Management (4-years) (P5167) | combined | 4 | Ph.D. | LF |
| Anesthesiology, Intensive Medicine and Pain Management (4-years) (P5167) | full-time | 4 | Ph.D. | LF |
| Archaeology (P7109) | combined | 4 | Ph.D. | FF |
| Archaeology (P7109) | full-time | 4 | Ph.D. | FF |
| Biochemistry (4-years) (P1416) | combined | 4 | Ph.D. | PřF |
| Biochemistry (4-years) (P1416) | full-time | 4 | Ph.D. | PřF |
| Biology (4-years) (P1527) | combined | 4 | Ph.D. | PřF |
| Biology (4-years) (P1527) | full-time | 4 | Ph.D. | PřF |
| Dentistry (4-years) (P5155) | combined | 4 | Ph.D. | LF |
| Dentistry (4-years) (P5155) | full-time | 4 | Ph.D. | LF |
| Dermatovenerology (4-years) (P5176) | combined | 4 | Ph.D. | LF |
| Dermatovenerology (4-years) (P5176) | full-time | 4 | Ph.D. | LF |
| Economic Policy and Administration (4-years) (P6224) | combined | 4 | Ph.D. | ESF |
| Economic Policy and Administration (4-years) (P6224) | full-time | 4 | Ph.D. | ESF |
| Economic Theory (4-years) (P6229) | combined | 4 | Ph.D. | ESF |
| Economic Theory (4-years) (P6229) | full-time | 4 | Ph.D. | ESF |
| Economy and Management (4-years) (P6230) | combined | 4 | Ph.D. | ESF |
| Economy and Management (4-years) (P6230) | full-time | 4 | Ph.D. | ESF |
| Education (P7501) | combined | 3 | Ph.D. | PdF |
| Education (P7501) | full-time | 3 | Ph.D. | PdF |
| Education (4-years) (P7536) | combined | 4 | Ph.D. | FF, PdF |
| Education (4-years) (P7536) | full-time | 4 | Ph.D. | FF, PdF |
| Finance and Accounting (4-years) (P6231) | combined | 4 | Ph.D. | ESF |
| Finance and Accounting (4-years) (P6231) | full-time | 4 | Ph.D. | ESF |
| General Medicine (P5103) | combined | 3 | Ph.D. | LF |
| General Medicine (P5103) | full-time | 3 | Ph.D. | LF |
| General Medicine (4-years) (P5149) | combined | 4 | Ph.D. | LF |
| General Medicine (4-years) (P5149) | full-time | 4 | Ph.D. | LF |
| General Theory and History of Arts and Culture (4-years) (P8111) | combined | 4 | Ph.D. | FF |
| General Theory and History of Arts and Culture (4-years) (P8111) | full-time | 4 | Ph.D. | FF |
| Geography (4-years) (P1314) | combined | 4 | Ph.D. | PřF |
| Geography (4-years) (P1314) | full-time | 4 | Ph.D. | PřF |
| Geology (4-years) (P1203) | combined | 4 | Ph.D. | PřF |
| Geology (4-years) (P1203) | full-time | 4 | Ph.D. | PřF |
| Gynaecology and Obstetrics (4-years) (P5168) | combined | 4 | Ph.D. | LF |
| Gynaecology and Obstetrics (4-years) (P5168) | full-time | 4 | Ph.D. | LF |
| Historical Sciences (4-years) (P7107) | combined | 4 | Ph.D. | FF |
| Historical Sciences (4-years) (P7107) | full-time | 4 | Ph.D. | FF |
| Hygiene, Preventive Medicine and Epidemiology (4-years) (P5169) | combined | 4 | Ph.D. | LF |
| Hygiene, Preventive Medicine and Epidemiology (4-years) (P5169) | full-time | 4 | Ph.D. | LF |
| Chemistry (4-years) (P1417) | combined | 4 | Ph.D. | PřF |
| Chemistry (4-years) (P1417) | full-time | 4 | Ph.D. | PřF |
| Informatics (4-years) (P1805) | combined | 4 | Ph.D. | FI |
| Informatics (4-years) (P1805) | full-time | 4 | Ph.D. | FI |
| Internal Medicine (4-years) (P5171) | combined | 4 | Ph.D. | LF |
| Internal Medicine (4-years) (P5171) | full-time | 4 | Ph.D. | LF |
| International Territorial Studies (4-years) (P6706) | combined | 4 | Ph.D. | FSS |
| International Territorial Studies (4-years) (P6706) | full-time | 4 | Ph.D. | FSS |
| Kinanthropology (4-years) (P7405) | combined | 4 | Ph.D. | FSpS |
| Kinanthropology (4-years) (P7405) | full-time | 4 | Ph.D. | FSpS |
| Matematics (4-years) (P1102) | combined | 4 | Ph.D. | PřF |
| Matematics (4-years) (P1102) | full-time | 4 | Ph.D. | PřF |
| Mathematics (P1101) | advanced state examination | 3 | Ph.D. | PřF |
| Medical Biology (4-years) (P5152) | combined | 4 | Ph.D. | LF |
| Medical Biology (4-years) (P5152) | full-time | 4 | Ph.D. | LF |
| Medical Biophysics (4-years) (P5181) | combined | 4 | Ph.D. | LF |
| Medical Biophysics (4-years) (P5181) | full-time | 4 | Ph.D. | LF |
| Medical Chemistry and Biochemistry (4-years) (P5158) | combined | 4 | Ph.D. | LF |
| Medical Chemistry and Biochemistry (4-years) (P5158) | full-time | 4 | Ph.D. | LF |
| Medical Microbiology and Immunology (4-years) (P5159) | combined | 4 | Ph.D. | LF |
| Medical Microbiology and Immunology (4-years) (P5159) | full-time | 4 | Ph.D. | LF |
| Medical Pharmacology (4-years) (P5157) | combined | 4 | Ph.D. | LF |
| Medical Pharmacology (4-years) (P5157) | full-time | 4 | Ph.D. | LF |
| Neurology (4-years) (P5172) | combined | 4 | Ph.D. | LF |
| Neurology (4-years) (P5172) | full-time | 4 | Ph.D. | LF |
| Neuroscience (4-years) (P5108) | combined | 4 | Ph.D. | LF |
| Neuroscience (4-years) (P5108) | full-time | 4 | Ph.D. | LF |
| Oncology (4-years) (P5162) | combined | 4 | Ph.D. | LF |
| Oncology (4-years) (P5162) | full-time | 4 | Ph.D. | LF |
| Ophthalmology (4-years) (P5153) | combined | 4 | Ph.D. | LF |
| Ophthalmology (4-years) (P5153) | full-time | 4 | Ph.D. | LF |
| Otorhinolaryngology (4-years) (P5137) | combined | 4 | Ph.D. | LF |
| Otorhinolaryngology (4-years) (P5137) | full-time | 4 | Ph.D. | LF |
| Patology (4-years) (P5173) | combined | 4 | Ph.D. | LF |
| Patology (4-years) (P5173) | full-time | 4 | Ph.D. | LF |
| Pediatrie (4-years) (P5174) | combined | 4 | Ph.D. | LF |
| Pediatrie (4-years) (P5174) | full-time | 4 | Ph.D. | LF |
| Philology (P7310) | combined | 3 | Ph.D. | FF |
| Philology (P7310) | full-time | 3 | Ph.D. | FF |
| Philology (4-years) (P7315) | combined | 4 | Ph.D. | FF |
| Philology (4-years) (P7315) | full-time | 4 | Ph.D. | FF |
| Philosophy (4-years) (P6147) | combined | 4 | Ph.D. | FF |
| Philosophy (4-years) (P6147) | full-time | 4 | Ph.D. | FF |
| Physics (4-years) (P1703) | combined | 4 | Ph.D. | PřF |
| Physics (4-years) (P1703) | full-time | 4 | Ph.D. | PřF |
| Physiology and Pathological Physiology (4-years) (P5156) | combined | 4 | Ph.D. | LF |
| Physiology and Pathological Physiology (4-years) (P5156) | full-time | 4 | Ph.D. | LF |
| Political Science (4-years) (P6705) | combined | 4 | Ph.D. | FSS |
| Political Science (4-years) (P6705) | full-time | 4 | Ph.D. | FSS |
| Psychiatry (4-years) (P5160) | combined | 4 | Ph.D. | LF |
| Psychiatry (4-years) (P5160) | full-time | 4 | Ph.D. | LF |
| Psychology (4-years) (P7703) | combined | 4 | Ph.D. | FF, FSS |
| Psychology (4-years) (P7703) | full-time | 4 | Ph.D. | FF, FSS |
| Radiology (4-years) (P5175) | combined | 4 | Ph.D. | LF |
| Radiology (4-years) (P5175) | full-time | 4 | Ph.D. | LF |
| Social Medicine (4-years) (P5161) | combined | 4 | Ph.D. | LF |
| Social Medicine (4-years) (P5161) | full-time | 4 | Ph.D. | LF |
| Social Policy and Social Work (4-years) (P6742) | combined | 4 | Ph.D. | FSS |
| Social Policy and Social Work (4-years) (P6742) | full-time | 4 | Ph.D. | FSS |
| Sociology (4-years) (P6707) | combined | 4 | Ph.D. | FSS |
| Sociology (4-years) (P6707) | full-time | 4 | Ph.D. | FSS |
| Special Education (P7506) | combined | 3 | Ph.D. | PdF |
| Special Education (P7506) | full-time | 3 | Ph.D. | PdF |
| Specialization in Pedagogy (P7507) | combined | 3 | Ph.D. | PdF |
| Specialization in Pedagogy (P7507) | full-time | 3 | Ph.D. | PdF |
| Specialization in Pedagogy (4-years) (P7537) | combined | 4 | Ph.D. | PdF |
| Specialization in Pedagogy (4-years) (P7537) | full-time | 4 | Ph.D. | PdF |
| Surgery (4-years) (P5170) | combined | 4 | Ph.D. | LF |
| Surgery (4-years) (P5170) | full-time | 4 | Ph.D. | LF |
| Theoretical Legal Sciences (4-years) (P6810) | combined | 4 | Ph.D. | PrF |
| Theoretical Legal Sciences (4-years) (P6810) | full-time | 4 | Ph.D. | PrF |
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