INTRODUCTION: The prevalence of the Functional Gastrointestinal Disorders (FGIDs) in Latino populations in resource-limited settings such as rural Central America is largely uninvestigated. The relationship of the FGIDs and dietary habits is unknown in this environment. METHODS: With population-based sampling, we administered the Rome IV questionnaire and a validated dietary questionnaire to a cross-section of the general adult population of rural Western Honduras. We estimated the prevalence of specific FGIDs and used logistic regression with Bonferroni adjustment to evaluate the relationship of each FGID diagnosis with particular dietary habits. RESULTS: We interviewed 815 subjects, of whom 151 fulfilled Rome IV criteria for an FGID (18.5% 95% CI 15.9-21.4%). The mean age was 40.6 years, of whom 58.7% were female. Gastroduodenal FGIDs were noted in 10.1%, with epigastric pain syndrome (EPS) more common than post-prandial distress syndrome (PDS), 8.5% versus 1.6%. Among the bowel disorders, functional abdominal bloating (FAB) was most prevalent (6.2%; 95% CI, 4.6-8.1), followed by irritable bowel syndrome (IBS, 3.5%, 95% CI 2.5-5.1; IBS-U 1.6%, IBS-C 1.2%, IBS-D 0.5%), functional diarrhea (FD, 3.4%) and functional constipation (FC, 1.1%). In multivariable logistic regression analysis, the diagnosis of any FGID was inversely associated with consumption of beans (OR 0.41, 95% CI 0.27-0.63, adjusted P = 0.009), driven by negative associations with IBS and FD. Overall vegetable consumption was associated with a lower prevalence of FD (OR 0.12, 95% CI 0.043-0.35, adjusted P = 0.018) and any diarrheal disorder (OR 0.11, 95% CI 0.42-0.31, adjusted P = 0.004). There was a trend toward association with all FGIDs for subjects who consumed greater than the mean daily intake of 4.6 corn tortillas per day, OR 1.74 (95% CI 1.22-2.50, adjusted P-value NS). CONCLUSION: FGIDs are prevalent in the resource-limited setting of rural Central America, with an altered distribution of specific FGIDs (common FAB, versus less common PDS, IBS, FC) compared with other global populations and urban Latin America populations. In this setting, with locally grown foods and limited diet variability, local dietary influences such as vegetable, bean, and tortilla intake may be important factors in specific FGIDs.