Tropical anemia can have multiple causes, whether socioeconomic, dietary, or infectious. In the Bolivian Chaco, soil-transmitted helminthiases (STH), malaria, and Chagas disease are potential infectious causes of anemia among school-aged children (SAC). Following years of preventive chemotherapy with mebendazole, the prevalence of STH among SAC living in that area is now negligible, whereas protozoan infections are still highly prevalent (81%); Hymenolepis nana is the most frequent intestinal helminth (∼13%). We present results of hemoglobin (Hb) assessment and the association between parasitic infections and Hb levels of that SAC population. Overall, 511 SAC (girls:boys ratio 1:1, mean age 9.4 years [95% confidence interval {CI}: 9.3-9.5]) had Hb levels measured by using a point of care testing (HemoCue® Hb 301 System; HemoCue, Angelhome, Sweden). The prevalence of anemia was 23% (117/511), with mean and median Hb level = 12.2 g/dL (95% CI: 12.1-12.3; range 9.2-15.4 g/dL). By multivariate analysis, H. nana infection was associated with an increased risk of anemia (odds ratio 2.9, 95% CI: 1.5-5.7, P = 0.002). Two samples (0.5%) were positive for Trypanosoma cruzi and none for Plasmodium spp. by polymerase chain reaction of the 439 children tested. Anemia is still a concern among SAC living in the Bolivian Chaco. Our findings call for a greater attention to fecal-oral emerging pathogens, such as H. nana, and highlight the importance of water, sanitation, and hygiene improvements for disadvantaged population such as those living in the Bolivian Chaco.