Bovine viral diarrhea virus (BVDV) is present in most cattle-raising countries around the world, and it has a negative economic impact in cattle herds. In Colombia, previous studies have estimated the prevalence of BVDV in specific locations. The aim of this study was to estimate the prevalence of BVDV in cattle herds located at several municipalities across the country and to identify the associated risk and protective factors.A cross-sectional study was carried out to investigate the prevalence of BVDV in Colombian cattle populations at farm and animal-levels. A total of 387 herds and 8110 animals located in seven different departments were included in this study.An animal- and farm-level prevalence of 36% and 69%, respectively, were estimated. A high variation for the farm-level prevalence was found among the municipalities studied. Moreover, seropositive cattle to the infectious bovine rhinotracheitis virus (odds ratio (OR)=2.38, p=0.0479) and Neospora caninum (OR=3.15, p=0.0122) were more likely to be seropositive for BVDV, while the practice of burning dead animals at the farm was identified as a protective factor (OR=0.17, p=0.014).The prevalence of BVDV varied more at farm-level compared to animal-level. Two risk factors and one protective factor were identified. The results of the current study are essential to understand the epidemiology of BVDV in Colombia, and to formulate strategies in the region to mitigate the impact of this virus on the productive and reproductive indicators of cattle farms at the regional level.