Dengue and Zika are mosquito-borne diseases caused by the vectors Aedes aegypti and Aedes albopictus, posing a significant public health threat to millions globally. Dengue is endemic in over 100 countries, including Guatemala. Effective vaccination trials are ongoing, but no specific antiviral treatment for dengue exists. Few studies have focused on the association between Dengue and Zika in Guatemala. To address this gap, we conducted a cross-sectional study utilizing census data from 2018, and the Guatemala Ministry of Health data. The unit of analysis in the study was the municipality, and there are 340 municipalities in Guatemala. The variables of investigation in the study included population density, percent literate, percent that use a cell phone, computer, and internet, percentage of the population, which is economically active, percentage of individuals with indoor plumbing, percent Mayan, the percent attending school, the mean annual minimum temperature, elevation in meters, and total yearly precipitation (mm). The study used dengue and zika cases from 2017. Univariate and multivariate negative binomial regression to predict the factors that caused Dengue and Zika virus incidence. There were 4210 cases of Dengue, and 546 cases of Zika Virus reported in Guatemala in 2017. Factors positively associated with dengue were cell phone, computer and internet use and minimum mean temperature, while Mayan and percentage of literate were negatively associated. For Zika, minimum mean temperature, cell phone, computer and internet use, and Dengue cases were positive predictors, while percent Mayan and percent literate were negatively related. In conclusion, this study concludes that the complex interplay between socioeconomic and environmental factors influenced the transmission of Zika Virus and Dengue in Guatemala. The findings underscore the importance of developing targeted interventions and conducting further research to explore individual-level factors and potential confounding variables for effectively preventing and controlling the transmission of these viruses in Guatemala and other regions.