The issue of whether to establish Specialist Chambers within the Kosovo justice system for alleged war crimes committed in Kosovo has been, arguably, one of the most heated debates not only from a political and social point of view, but also from a legal one. While the required amendments in the Constitution and several laws of Kosovo necessary to establish the Specialist Chambers in furtherance of the agreement dated 14 April 2014 between the Republic of Kosovo and the European Union on the Mission of the European Union Rule of Law Mission in Kosovo (“EULEX”) will certainly create heated debates in the political level, one may argue that the legal issues that are expected to be encountered when the Specialist Chambers will be operational, may be even more pressing. This is in consideration of the peculiar nature of the Specialist Chambers, which are meant to have their basis within the laws of Kosovo, but at the same time, be independent from them and from control of Kosovo authorities. The purpose of this article is to delineate the possible legal issues that might confront the Specialist Chambers of Kosovo. Its main argument is that, while the Specialist Chambers seem to follow the experience of other hybrid internationalised courts, it still differs from them in some aspects. The challenges that the new Specialist Chambers may need to tackle deal with its jurisdiction and position within the Kosovo Judicial system, and its legitimacy and legal basis.