Background Mycobacterium avium subspecies paratuberculosis (MAP) causes chronic, wasting, and progressive enteritis in cattle, bringing significant economic losses in livestock industries. MAP has spread worldwide mainly due to movement of animals. The objective of this study was to determine the MAP seroprevalence in cattle in the Xinjiang Uygur Autonomous Region, Northwest China, and evaluate the difference between intensive farming herds (cattle number in a herd is more than 200, and the cattle cannot have access to pasture) and free-range herds (the cattle are bred by individual households, a herd is defined as the cattle are bred in a village or town in this study). Results A total of 3157 serum specimens were collected from 42 herds in nine different regions. This included 1481 specimens from 18 intensive farming herds in four regions and 1676 specimens from 24 free-range herds in six regions. Antibody against MAP was tested with commercial ELISA test kits. The results showed that the overall apparent prevalence was 4.8% (95% CI, 4.1 to 5.6%) at animal level, and 50.0% (21/42) at herd level. The apparent prevalence in intensive farming herds and free-range herds were 9.5% (141/1481) and 0.7% (11/1676) at the animal-level, 88.9%(16/18) and 20.8% (5/24) at herd level, respectively, with a significant statistical difference between these two farming modes (p