Bovine paratuberculosis causes chronic, incurable diarrhea and weight loss, resulting in decreased cattle production. The disease is caused by Mycobacterium avium subsp. paratuberculosis (MAP), an obligate intracellular mycobactin-dependent mycobacterium that replicates slowly in the host and has heightened environmental resistance. In countries where the disease is found and the damage has been quantified, direct and indirect economic losses are extremely high. Local epidemiological data is of paramount importance for the implementation of control programs. Our objective was to verify whether paratuberculosis is present in commercial dairy herds in different mesoregions of RS. Therefore, a prospective, cross-sectional and observational study was performed on dairy cattle from five mesoregions of the RS state, Brazil. Milk samples taken from individual cows on commercial farms were tested using indirect ELISA tests and classified as negative, suspicious, or positive. In herds containing at least one positive cow, we conducted convenience sampling of feces directly from the rectal ampulla to identify MAP through PCR. Of the 362 cows tested, 20 were seroreactive for paratuberculosis from two mesoregions. The PCR tests were all positive; cows with a negative ELISA and positive PCR results probably indicate that the MAP was ingested and eliminated without causing infection. We found that paratuberculosis is likely endemic in the northwest and northeast mesoregions.