Among the most sensitive issues of transitional justice there are, on one hand, the co-relation between the criminal penalty for violating international humanitarian law and human rights law, and on the other hand, the implementation of an alternative institution, such as amnesty, in the context of achieving the main goal of national reconciliation and the peaceful development of the country. The pragmatic aspect of transitional justice is based on accepting the amnesty in various forms, while international law reminds states of their international obligations, either on a conventional or customary basis – to implement the institution of criminal liability against those who committed serious violations of international humanitarian law or human rights law. Today, the norms that constitute the nucleus of these two branches of law, are part of the category of norms with jus cogens character, which is recognized at both doctrinal and jurisdictional level.