The renewed interest in community participation in health research is linked to its potential for bridging gaps between research and practice. Its main attributes are the generation of knowledge that can lead to socially robust, long-lasting solutions and the creation of a co-learner relationship between researchers and research users. Following this philosophy, Ecohealth has evolved into a specialized framework for participatory research on the impact of pollution on ecosystems and human health. However, its principles pose considerable challenges. Its outcomes are strongly influenced by contextual factors that are impossible to control for ahead of time.This paper describes how the Ecohealth principles were applied to an epidemiological study of heavy metals exposure among indigenous communities of the Peruvian Amazon. It illustrates how knowledge generated from participatory research does not necessarily imply solving a public health problem. This study aimed to contribute to the understanding of the benefits and barriers of following the basic principles of the Ecohealth approach, and assist researchers working in similar contexts.