Apart from the main Postgraduate Programme in Computer Science and Engineering which is organised and offered by the Department of Computer Science, it also participates in three interdisciplinary MSc programmes:

- Brain and Mind   https://brain-mind.med.uoc.gr/
 
- Data Analysis and Machine-Statistical Learning https://mscs.uoc.gr/damsl/
 
- Biomedical engineering https://mscs.uoc.gr/bme-crete/