Non-communicable diseases are the new health epidemics in developing countries due to increased life expectancy, and changes in lifestyle and dietary habits of the population. The Atahualpa Project was designed as a multi-step population-based cohort study designed to reduce the increasing burden of these conditions in rural Ecuador. The first step of the study followed a 3-Phase design, aimed to get information on demographics and cardiovascular risk factors of Atahualpa residents aged ≥40 years, as well as to assess the prevalence of stroke and ischemic heart disease. During Phase I, participants were screened with standardized questionnaires to evaluate their cardiovascular health and to identify those with suspected stroke or ischemic heart disease. In Phase II, neurologists and cardiologists examined suspected cases of stroke or ischemic heart disease, as well as a random sample of matched negative individuals, to assess prevalence of these conditions. In Phase III, patients with diagnosis of stroke and ischemic heart disease underwent complementary tests for achieving more specific diagnosis. Implementation of public health strategies directed to improve the cardiovascular health status of a given population must be based on studies evaluating specific risk factors at regional levels. Epidemiologic surveys such as the Atahualpa Project may prove cost-effective for improving the cardiovascular health status of people living in Latin American rural villages by increasing the knowledge on the particular needs of these populations.