Introduction: The prevalence of allergic diseases is increasing worldwide, affecting about 30% of the population in low to middle-income countries. Research trends on allergic diseases within rural pediatric populations of Latin American countries is scarce. This study aimed to determine the prevalence of allergic diseases (allergic rhinitis, asthma, and atopic dermatitis) and their associated factors using the International Study of Asthma and Allergies in Childhood-III (ISAAC-III) questionnaire in school-aged children from two rural municipalities in Colombia.Materials and methods: This is a cross-sectional study. The ISAAC-III questionnaire was applied to school-aged children attending elementary schools in the municipalities of Soracá and Palmas del Socorro during 2018. The questionnaires were applied to adolescents aged 13–14 years and the parents of 6–7 years old children. Associations were estimated via bivariate and multivariate analysis. Results: Among 261 school-aged children (58.2% adolescents), the prevalence of allergic dis-eases was: allergic rhinitis 11.49% (95% CI: 8.05–15.78), asthma 8.81% (95% CI: 5.82–12.7), and atopic dermatitis 6.13% (95% CI: 3.69–9.53). Associated factors for allergic rhinitis included: female sex (PR: 2.68, 95% CI: 1.17–5.26), asthma (PR: 4.69, 95% CI: 1.96–8.31), atopic dermatitis (PR: 3.55, 95% CI: 1.09–7.83), and higher maternal education (PR: 4.16, 95% CI: 1.45–8.25).Conclusions: The prevalence of allergic diseases in this rural pediatric population was lower compared with that of the previous reports from urban populations. Associated factors found in this study support previous studies. Research addressing modifiable environmental associ-ations is so far scarce in Latin America; further studies are needed to reduce the burden of these diseases in rural populations.