Paratuberculosis (Johne's disease), a chronic wasting disease caused by Mycobacterium avium subspecies paratuberculosis (MAP), is a major cause of economic loss in the cattle industry. In Korea, national monitoring of breeding stock for MAP has been implemented. In this study, we report the results of serological testing to determine the prevalence of MAP in breeding stock of Korean native and dairy cattle during 2008 and 2009. A total of 3,927 serum samples were submitted (3,692 Korean native cattle and 235 dairy cattle) to Animal Disease Diagnostic Division, Animal, Plant and Fisheries Quarantine and Inspection Agency. The samples were classified into four different age groups for MAP; group 1 (≤2 year, n = 1,509), group 2 (>2 years to≤3 years, n = 486), group 3 (>3 years to ≤4 years, n = 441), and group 4 (>4 years, n = 1,491). Overall seroprevalence of MAP in this study was 0.5% (21/3,927), which was much lower than that of conventional cattle (1.2-16.4%) in Korea. Also, the seroprevalence was determined by age groups: three of group 1 (0.2%), two of group 2 (0.4%), three of group 3 (0.7%), and 13 of group 4 (0.9%) were seropositive for MAP, respectively. Although seropositive samples were found in all age groups, the seroprevalence tended to increase with age. Our study showed that the seroprevalence of MAP in pure-bred breeding dairy cattle (0%) was lower than that in pure-bred breeding Korean native cattle (0.6%).