Paratuberculosis is a disease caused by Mycobacterium avium subsp. paratuberculosis (MAP). In domestic ruminants, MAP infection is largely sub-clinical, but can result in chronic diarrhea leading to emaciation and death. A survey of MAP was carried out in a non-vaccinated sheep population from Nayarit, México to estimate seroprevalence and histopathological findings. The aim was also to estimate the intra-herd correlation (re) and design effect (D) of MAP seropositivity and to determine the association of the disease with some animal-level risk factors. Serum samples from 368 sheep older than 2 years in 38 herds were evaluated using an indirect ELISA assay. Eleven of the 38 herds had at least one seropositive animal and 19 animals with a total of 368 tested positive for MAP (5.6%). The histological alterations found were characterized by enteritis and granulomatous lymphadenitis indicating that the death of the animal was caused by MAP infection.