In 2005, Amazonas State, Brazil, showed hyperendemic leprosy detection coefficients and prevalence with medium endemicity. Although this State has the largest indigenous population in Brazil, there are no data on the leprosy profile in these groups. This study aimed to describe and analyze the epidemiological characteristics of leprosy case reporting in the municipalities (counties) of Autazes, Eirunepé, and São Gabriel da Cachoeira, comparing indigenous and non-indigenous findings according to target variables. A total of 386 cases reported to SINAN from 2000 to 2005 were analyzed. Mean detection rates were 3.55, 14.94, and 2.13/10,000 (among non-indigenous) and 10.95, 1.93, and 0.78/10,000 (among indigenous peoples) in Autazes, Eirunepé, and São Gabriel da Cachoeira, respectively. Paucibacillary cases predominated among both indigenous and non-indigenous populations; however, dimorphous cases represented one-third of notifications. Despite coverage limitations and underreporting, the findings suggest that leprosy is a major public health problem for indigenous populations in Amazonas State. Classification according to race/ethnicity has been a useful tool for solving health inequalities.