The current configuration of Indigenous peoples’ health in Brazil is the result of a complex historical trajectory marked by cultural and territorial conflicts associated with the country’s internal colonialism, environmental degradation, and, in many cases, state failures. For Indigenous peoples, this process contributed to considerable delays in benefiting from the social progress achieved throughout the country in recent decades, particularly in the fields of health, education, housing, and sanitation. Case studies in different ethnic groups since the 1990s have highlighted contexts of health inequalities marking the distinction between being Indigenous and non-Indigenous in Brazil. In other words, being Indigenous implies greater chances of not living beyond the first year of life, suffering from under-nutrition and anemia during the growth period, living with high burden of infectious and parasitic diseases, and being exposed to a rapid process of nutritional transition responsible for the emergence of chronic diseases such as obesity, hypertension, and diabetes mellitus. At the community level, concrete actions taken by the country’s Indigenous health care subsystem are modest and conservative, and therefore not able to deal with the complexity of real health needs in the diverse sociocultural, environmental, and epidemiological contexts characterising the country’s 300 Indigenous ethnic groups. The main objective of this contribution is to outline the overall health profile and patterns of iniquity among Brazil’s Indigenous population, with emphasis on results from the First National Survey of Indigenous People’s Health and Nutrition in Brazil, conducted in 2008-2009.