Background Colombia has officially adopted the parasite density levels of severe malaria established by the WHO (>50,000 parasites/μl). These values have been inferred from areas of high transmission in Africa and are not consistent with the dynamics of low and unstable transmission in Colombia. The objective of this study was therefore to determine the parasite density values observed in patients with severe malaria and their distribution in the different ecoepidemiological regions of Colombia. Methods A retrospective and descriptive study of confirmed cases of severe malaria was conducted in endemic areas of malaria in Colombia over the period 2014-2017. Data were collected from secondary sources of the Subnational Programs of Malaria Prevention and Control. Person, place, and time variables were selected. The official definition of severe malaria was adopted, and compliance with these criteria was determined. Univariate and bivariate analyses were conducted with absolute and relative frequency measures, and the relevant statistical tests were applied. Results The overall parasite density values in Colombia showed a geometric mean of 5,919 parasites/μl (95% CI: 5,608-6,248). By parasite species, the values were 6,151 (95% CI: 5,631-6,718) for Plasmodium falciparum and 5,815 (95% CI: 5,428-6,230) for Plasmodium vivax. The highest parasite density values were recorded in the Amazon ecoepidemiological region (8,177; 95% CI: 6,015-11,116), and the lowest values were recorded in the Andean region (5,026; 95% CI: 2,409-10,480). Conclusions In endemic areas of low and unstable malaria transmission in the Colombian territory, the parasite density levels observed in populations with severe malaria are lower than the officially established values. The parasite density criterion is not really a relevant criterion for the definition of severe cases in Colombia and it certainly not be used to make a clinical decision about the severity of the disease.