Objective: To determine the prevalence of intestinal parasitism and relevant public health zoonotic ectoparasites in canines of indigenous communities of the Colombian Amazon. Materials and methods: This study included 421 canines from 68 communities, whose owners participated voluntarily in educational talks, interviews, and epidemiological surveys. Fecal samples were obtained by rectal palpation, and they were processed using the formalin-gasoline concentration technique. Double-blind triplicate microscopic analysis was carried out. Results: Parasite infection occurred in 89.8% of the samples, 57.7% protozoans and 73.9% helminthes. Hookworms were noteworthy, including Toxocara spp., Strongyloides spp., Alaria spp., and Giardia spp., among others. Ectoparasites were found in 32.8% of the cases. Conclusion: Our study showed the potential risk of transmission of zoonotic infections by canine parasites and the possibility of jungle transmission of the rabies virus, which require intervention with preventive and control programs by the health sector.