BACKGROUND: Leptospirosis is an important zoonosis with worldwide distribution caused by pathogenic bacteria of the genus Leptospira. The North American mink (Neovison vison) has an important role in the environmental contamination with Leptospira, as minks live in aquatic environments and are the predators of rodents. FINDINGS: Blood and kidney samples were obtained from 57 minks in Southern Chile 39° S to 45° S. Pathogenic species of Leptospira were detected by PCR on 31/57 minks. To determine the species, we sequenced the 16S ribosomal RNA (rRNA) gene on nine of the positive samples. We predicted two pathogenic species: Leptospira interrogans (five samples) and Leptospira borgpetersenii (four samples). CONCLUSIONS: This study showed that the American mink presents pathogenic species of Leptospira and confirm important environmental contamination of Patagonian rivers and lakes with pathogenic Leptospira.