Background: Leishmaniasis is considered a Neglected Tropical Disease (NTDs) and one of the most frequently reported tegumentary parasitic diseases among refugees and internally displaced populations (IDPs) in Africa and Asia, nevertheless there is lack of studies about it in Latin America, even in Colombia, the country with the highest number of IDPs in the in the world. Methods & Materials: This ecological study assessed incidence and differences, of leishmaniasis between general population and IDPs in Colombia and its departments (32) during 2007–2014. Epidemiological data was collected from the National Surveillance System (SIVIGILA-SISPRO), retrieving the codes for tegumentary (CL and MCL) and visceral leishmaniasis (VL) in both populations. We estimated leishmaniasis incidence rates on both populations (cases/100,000 pop), using reference population of the IDPs (official record of the Secretary of Social Welfare) and the general population (from the national statistics institute, DANE). Incidence rates ratios were calculated comparing both populations. Results: In general population, 82,012 cases of leishmaniasis occurred (98.43% CL, 1.32% MCL and 0.24% VL) (179.13 cases/100,000 pop, 95%CI 178.0–180.0) while 2,434 among IDPs (98.02% CL, 1.97% MCL and 0.37% VL) (797.2 cases/100,000 pop, 95%CI 765.0–829.0). Leishmaniasis was 4.5 times higher among IDPs than in general population (p < 0.05) (reaching up to 7 times higher in 2013 and during that year 132.7 times higher in Caldas department). IDPs leishmaniasis cases occurred in 75.6% in males and 24.4% in females. By age groups, 69.2% were <40 y-old (4.4% <10 y-old). All cases of VL corresponded <20 y-old. Conclusion: This study evidenced a significantly higher leishmaniasis incidence among IDPs, being higher in male and below 40 y-old, when compared with general population in the same territories, which would be expectable given the socioenvironmental conditions in which these subjects have lived. The presence of VL corresponding to pediatric internally displaced persons should be alerted. This has relevant implications for screening, diagnosis and management among IDPs, especially in still highly endemic areas. More studies are required to improve the understanding of tropical diseases among vulnerable populations, as well to provide better medical interventions and for the development of public policies in countries, such as Colombia, with IDPs.