This article aims to give an overview of how human rights violations that occurred during the Homeland War in Croatia are redressed by conducting criminal prosecution in the Republic of Croatia. Namely, criminal prosecution as one of the elements of transitional justice is essential not only for establishing the accountability of war crime perpetrators, but also as a warning that such violations shall not be tolerated in the future. Moreover, drawing on the jurisprudence of the European Court of Human Rights, this article examines how the efforts made by national prosecution bodies to investigate war crimes are assessed by this court. It concludes with the idea that both prosecution of war crimes and protection of human rights, as guaranteed by The Convention for the Protection of Human Rights and Fundamental Freedoms and the European Court of Human Rights, seek to achieve the same goal, i.e. protecting the most basic human rights of the war crimes victims and other individuals.