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We performed a cross-sectional study of Trypanosoma cruzi seroprevalence in 14 communities in three provinces of Ecuador and estimated the magnitude of the association of seropositive individuals within households. A total of 3,286 subjects from 997 households were included. Seroprevalence was 5.7%, 1.0%, and 3.6% in subjects in the Manabí, Guayas, and Loja provinces, respectively. Seroprevalence increased with increasing age in Manabí and Guayas, whereas in Loja, the highest prevalence occurred in children ≤ 10 years of age. In the coastal provinces, clustering of seropositives within households was not observed after adjustment for other household factors. However, in the Andean province of Loja, the odds of seropositivity were more than two times greater for an individual living in a household with another seropositive person. Our results indicate that transmission of T. cruzi is ongoing in Ecuador, although intensity of transmission and mechanisms of interaction between humans and the insect vectors of disease vary between geographic regions.