Background: In Colombia, taeniasis and cysticercosis have been significantly reduced over the past decades, however still reported with implications for public health and travel medicine. Methods: An observational, retrospective study, in which the incidence of taeniasis and cysticercosis (ICD-10 codes B68s/B69s) in Colombia, 2009–2013, was estimated based on data extracted from the Individual Health Records System (Registro Individual de Prestación de Servicios, RIPS) was performed. The Geographic Information System (GIS) generated national maps showing the distribution of taeniasis and cysticercosis by department by year. Results: During the period, 3626 cases were reported (median 796/year), for a cumulative crude national rate of 7.7 cases/100,000pop; 58.2% corresponded to male; 57% were <40 year-old (10.2% < 9.9 year-old). Cases were 57.6% neurocysticercosis, the rest were taeniasis due to T. solium, T. saginata, ocular cysticercosis and cysticerci in other organs. Bolivar, a touristic department, had the highest cumulated incidence rate (16.17 cases/100,000pop), as also evident across the map series developed in this study. Conclusion: Despite the limitations of this study, data presented provide recent estimates of national taeniasis and cysticercosis incidence in the country useful in public health and for travel medicine practitioners, as some highly touristic areas presented higher disease incidence. Improved control, particularly of taeniasis, should be an attainable goal, which among other strategies would require improved sanitation and health education to prevent transmission, but also enhanced surveillance.