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Epilepsy is a major health issue in rural areas of developing countries. However, heterogeneity of epilepsy prevalence in different studies precludes assessment of the magnitude of the problem. Using similar protocols, two population-based surveys were conducted 12 years apart (2003 and 2015) in a rural Ecuadorian village (Atahualpa). The only difference was a higher people compliance with interviewers during the second survey. Epilepsy prevalence in the 2003 survey was 13.5 per 1,000 (18/1,332) in villagers aged ≥20 years. This rate increased to 26.8 per 1,000 (41/1,530) in the 2015 survey. Thirty-three persons with epilepsy detected during the second survey lived in the village in 2003; six of them had seizures starting after 2003. Of the remaining 27 cases, 13 (48%) denied their problem during the first survey. Further interview revealed that denial was related to lack of confidence with unacquainted field personnel. Social Desirability Scale-17 scores were lower in those who admitted having epilepsy than in those who denied their condition (p = 0.048). Lack of confidence with interviewers and a social desirability bias account for a sizable proportion of epilepsy denial in the study population, and may explain heterogeneity of epilepsy prevalence reported in studies conducted in poor rural settings.