BACKGROUND Giardia intestinalis is a protozoan parasite that causes a gastrointestinal infection known as giardiosis, which is transmitted primarily through fecal-oral contamination. Genetic studies of axenically cultivated Giardia isolates have identified two major genetic groups distributed throughout the world. In the present study 24 native strains of the parasite were analyzed by the RAPD technique (Random Amplified Polymorphic DNA). OBJECTIVE To determine the level of polymorphism and the complexity of Giardia intestinalis circulating strains in specific areas of Colombia. METHODS The RAPD method was used, as it allows for a quick, simple and reliable analysis that requires no prior knowledge of the genetics of the parasite. A RAPD analysis was conducted on native isolates collected in Colombia between 1997 and 2001, established in continuous cultures. Several primers were tested separately, in order to enhance the capacity for discrimination of the method. RESULTS Of the 24 strains that were included in the study, 22 were arranged in independent clusters. The strains that were from the same geographic area and collected at about the same time, generally displayed highly similar but distinguishable RAPD patterns. Clones isolated from a strain were analyzed as well, and it was possible to differentiate them molecularly. CONCLUSIONS The studied strains showed to belong to genotype A . The results suggest that the Colombian strains studied consist of a heterogeneous mixture of closely related populations.