In recent years there have been many hot debates in Macedonia in terms of systemic changes in the area of higher education. We can say that the Government has increased the standards for professors and research activities in general with the adoption of new law amendments concerning higher education regulations. The question is whether the government is more interested for changes rather than universities? But, the strengthening of normative standards does not necceseraly mean that the transition from a more conventional to a more modern approach in PhD studies would also mean a complete implementation of the Salzburg Principles. Third-study education issues in Macedonia are still under constructions and need some changes regarding ethical standards in research and plagiarism policies. We can't say that it's completely reformed yet. Macedonia has implemented a part of what the three-year system and the EUA (European University Association) imply even with the old mentor system of PhD studies. The new PhD candidates have to present their research progress presentations regarding their PhD thesis, take part in scientific conferences, publish their work in journals etc. In this way independent work, transparency and performance would improve. The new system -the Doctoral School -which started in the academic year 2012-2013 is based upon scientific research, independent work, transparency, student and staff mobility, projects, etc. This will be a step forward towards the European model of knowledge and experience. In the Macedonian case the question is whether these innovations will improve the quality of education within these structured programs and doctoral schools. The new Bologna-based approach not only represents a challenge but also a path with many struggles. This is another qualitative challenge for scientific researchers and especially for the new PhD candidates.