Introduction Guatemala is the most populous country in Central America and a setting with unique opportunities for aging research. Approximately 40% of Guatemala's population is Indigenous Maya, who together speak 22 Mayan languages. Currently, there is no population-based aging study in Guatemala and few aging studies in Latin America among Indigenous populations. The Longitudinal Study of Aging in Guatemala (ELEGUA) aims to address these gaps by developing a nationally representative, population-based, longitudinal aging study modeled on the Health and Retirement Study and the Harmonized Cognitive Assessment Protocol, adapted to the cultural and linguistic context of Guatemala. The objective of this protocol is to describe the rationale and design of the ELEGUA pilot survey. Methods and analysis The ELEGUA pilot was a cross-sectional household survey of adults aged 40 years or older in Tecpan, Guatemala. Tecpan was chosen because its diverse population facilitated testing of study procedures in both Spanish and Kaqchikel, a common Mayan language. The survey included up to 600 households sampled using a multistage stratified cluster design. Within each household, one individual aged 40 years or older was selected, with oversampling of adults aged 55 years or older. This respondent completed a comprehensive questionnaire, including detailed cognitive tests, and provided physical measurements and a venous blood sample. Household respondents provided information on household economics and family structure, and an informant reported on the individual respondent's cognitive function. Data were collected using a computer-assisted personal interviewing system. Planned analyses include survey-weighted descriptive statistics and psychometric evaluation of the cognitive assessments. Ethics and dissemination Ethics approval was obtained from the ethics committees of the Institute of Nutrition of Central America and Panama, Maya Health Alliance, and the University of Michigan. Results will be disseminated through publications in peer-reviewed journals and presentations to local, national, and international audiences.