Study programmes
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| Faculty | Study type | Name of the study program | Language of instruction | Study form | ||
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| Catholic Theological Faculty | Master's | Catholic Theology | Czech | full-time |
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| Faculty of Law | Master's | Law and Jurisprudence | Czech | full-time |
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| Faculty of Law | Master's | Law and Jurisprudence | English | full-time |
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| First Faculty of Medicine | Master's | General Medicine | Czech | full-time |
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| First Faculty of Medicine | Master's | Dentistry | Czech | full-time |
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| First Faculty of Medicine | Master's | Dentistry | English | full-time |
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| First Faculty of Medicine | Master's | General Medicine | English | full-time |
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| Second Faculty of Medicine | Master's | General Medicine | Czech | full-time |
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| Second Faculty of Medicine | Master's | General Medicine | English | full-time |
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| Third Faculty of Medicine | Master's | General Medicine | Czech | full-time |
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| Third Faculty of Medicine | Master's | General Medicine | English | full-time |
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| Faculty of Medicine in Pilsen | Master's | Dentistry | Czech | full-time |
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| Faculty of Medicine in Pilsen | Master's | General Medicine | Czech | full-time |
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| Faculty of Medicine in Pilsen | Master's | General Medicine | English | full-time |
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| Faculty of Medicine in Pilsen | Master's | Dentistry | English | full-time |
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| Faculty of Medicine in Hradec Králové | Master's | Dentistry | Czech | full-time |
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| Faculty of Medicine in Hradec Králové | Master's | General Medicine | Czech | full-time |
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| Faculty of Medicine in Hradec Králové | Master's | Dentistry | English | full-time |
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| Faculty of Medicine in Hradec Králové | Master's | General Medicine | English | full-time |
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| Faculty of Pharmacy in Hradec Králové | Master's | Pharmacy | Czech | full-time |
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| Faculty of Pharmacy in Hradec Králové | Master's | Pharmacy | English | full-time |
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| Faculty of Education | Master's | Teacher Training For Primary Schools | Czech | combined |
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| Faculty of Education | Master's | Teacher Training For Primary Schools | Czech | full-time |
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