Transitional justice is resorted to within the framework of transition from armed conflict to peace and from authoritarian regimes to the democratic ones. To reach the aims of transitional justice and to better integrate the needs and perspectives of the indigenous peoples that very often are victims of serious human rights violations in the transitional context, as well as the colonisation context, indigenous instruments of justice may be utilised. As such they may be treated as complementary to other transitional justice mechanisms. The article aims to find a new perspective on the complementary role of the indigenous justice and the State justice systems within the framework of transitional justice as well as to take into account the indigenous peoples’ needs and customs. The overall aim of the paper is to answer the question whether it is desirable for such indigenous justice instruments to complement the State justice systems through a better integration of the needs and customs of indigenous peoples. In the concluding remarks, a model of complementarity model of transitional justice that includes indigenous instruments will be proposed.