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In recent years the European countries have created a standard form for their Higher Education Systems, the Standards and Guidelines for Quality Assurance in the European Higher Education Area (ESG). In this paper, we have analyzed the levels of the Accreditation Process applied to the Higher Education Institutions (HEIs) in Kosovo and Albania, and the compliance to the ESG guidelines. Furthermore, throughout the entire paper, we have made a comparison of the standards of the Accreditation Process for the HEIs in Kosovo and Albania. In order to capture these stages, we have surveyed both the accreditation agencies and the HEIs in Kosovo and Albania. From this analysis, we came to the conclusion that the accreditation process in Kosovo and Albania for the HEIs are in compliance to the ESG standards, and there is no a huge difference appearing, although Kosova is not part of Bologna Process. The paper gives hands-on information about the accreditation process of the HEIs in Kosovo and Albania that will be in the interest of all Higher Education System designers and developers of these two countries, but also for other transitions countries.