The aim of the present work was to complete an exposure assessment in three Mexican indigenous communities using the community-based health risk assessment, which is the first step in the CHILD framework. We used 1-hydroxypyrene (1-OHP) as an exposure biomarker to polycyclic aromatic hydrocarbons (PAHs) and trans, trans-muconic acid (t,t-MA) as an exposure biomarker to benzene, persistent organic pollutants (POPs), lead, manganese, arsenic, and fluoride. Anthropometric measurements were also taken. In these communities, high percentages of children with chronic malnutrition were found (28 to 49 %) based on their weight and age. All communities showed a high percentage of children with detectable levels of four or more compounds (70 to 82 %). Additionally, our results showed that in indigenous communities, children are exposed to elevated levels of certain environmental pollutants, including manganese with 17.6, 16.8, and 7.3 μg/L from SMP, TOC, and CUA, respectively. Lead and HCB levels were similar in the indigenous communities (2.5, 3.1, and 4.2 μg/dL and 2.5, 3.1, and 3.7 ng/mL, respectively). 1-OHP and t,t-MA levels were higher in TOC (0.8 μmol/mol of creatinine, 476 μg/g of creatinine, respectively) when compared with SMP (0.1 μmol/mol of creatinine, 215.5 μg/g of creatinine, respectively) and CUA (0.1 μmol/mol of creatinine, 185.2 μg/g of creatinine, respectively). DDE levels were 30.7, 26.9, and 9.6 ng/mL in CUA, SMP, and TOC, respectively. The strength of this study is that it assesses exposure to pollutants with indications for the resultant risk before an intervention is made by the CHILD program to manage this risk in the indigenous communities. Considering the large number of people, especially children, exposed to multiple pollutants, it is important to design effective intervention programs that reduce exposure and the resultant risk in the numerous indigenous communities in Mexico.