Although indigenous peoples are an important and large group of citizens in Latin America, the region seemed to be neglecting them for many decades. This has changed recently, thanks to both internal and external factors. The agenda for indigenous peoples found its place also in Latin American regional organizations. The paper focuses on two of them: the Andean Community (CAN) and the Southern Common Market (Mercosur). The aim of the research is to compare their policies on indigenous peoples by answering the following research questions: 1) What share of the population of the member countries of CAN and Mercosur do autochthonous inhabitants constitute?; 2) What actions for indigenous peoples were undertaken in the member countries of CAN and Mercosur?; 3) Since when and to what extend have CAN and Mercosur been working on the agenda for indigenous peoples?; 4) Which of the two organizations is more active in the abovementioned field and what are the probable causes of the differences in their engagement? The research uses a comparative approach, and it is mainly based on critical analysis of primary and secondary sources.