ABSTRACT INTRODUCTION Despite growing research interest in the epidemic of chronic kidney disease of nontraditional etiology (a distinct form of chronic kidney disease disproportionately affecting agricultural populations across Mesoamerica—Central America and southern Mexico), its etiology remains poorly understood. OBJECTIVE Elucidate factors that impact researchers’ efforts to understand the epidemic of chronic kidney disease of nontraditional etiology. METHODS Semistructured interviews were conducted with 39 international researchers, selected based on their publications and participation in conferences about chronic kidney disease of nontraditional etiology. Interviews were conducted from May through September of 2015 in English or Spanish by video conference, telephone or in person. Interviews were audio recorded, transcribed, and analyzed iteratively using content analysis. RESULTS Of 39 researchers interviewed, 30.8% were women, 84.6% had a medical and/or doctoral degree and 74.3% had ≥6 years’ experience carrying out research on chronic kidney disease of nontraditional etiology. Three major themes were identified related to factors affecting research progress. The first, influence of state and private interests, concerned perceptions that sugar industry and some governments in Mesoamerica dismissed, hindered, intimidated and inaccurately represented research on chronic kidney disease of nontraditional etiology. The second, limited material and human resources, had to do with scarcity of stable, impartial funding and adequate in-country research infrastructure. Researchers were largely funded by nontraditional sources (charitable organizations, private donations, sugar industry in Mesoamerica, personal funds) or not funded at all. The third, logistical challenges across study lifetimes, referred to barriers such as unwieldy approval mechanisms, gang interference and publication hurdles. CONCLUSIONS Producing high quality and clinically relevant studies to address chronic kidney disease of nontraditional etiology in the resource-scarce Mesoamerican research climate has been fraught with challenges. These findings contextualize the progress that has been made in understanding chronic kidney disease of nontraditional etiology to date and highlight the need for public health and biomedical organizations to support researchers’ ongoing efforts to engage all stakeholders in addressing the epidemic, disseminate their research findings and identify feasible strategies for addressing the community-wide suffering caused by chronic kidney disease of nontraditional etiology.