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What if after the Foundation Course I want to apply to another Italian (or foreign) University which is not the University of Pisa?

If you want to apply to another University you should ask them in advance what are the academic requirements for the enrollment, apart from having a High School Diploma/Secondary School Leaving Qualification and the Foundation Course Certificate (Humanities/Science).

The Foundation Course is recognized by the Italian government as a way to fill the gap between the secondary school and the University, but each University holds a certain degree of autonomy regarding the admission of its students, so please contact the Universities of your interest interest  in advance and ask them whether or not they will accept you with your Secondary School Leaving Qualification plus a Foundation Course certificate.