Paratuberculosis (Johne’s disease), an enteric disorder in ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP), causes economic losses in excess of $200 million annually to the US dairy industry. To identify genomic regions responsible for susceptibility to MAP infection in Jersey cattle, a case-control, whole genome association study was carried out. Blood and fecal samples were collected from approximately 5000 mature cows in 30 commercial Jersey herds from across the US. All animals were tested initially with a serum ELISA test, and incidence of positive results within herd ranged from 0.03 to 0.30. All animals with positive ELISA test results were also tested with a fecal culture test. Case definition was a positive test result for both ELISA and fecal culture tests. For each case, a matching control from the same herd (negative to both tests) was chosen based on the proximity of its date of birth to the case’s birth date. A total of 878 animals (447 cases, 431 controls) were successfully genotyped with the Illumina Bovine SNP50 BeadChip. Whole-genome association analysis was performed using the genomic GRAMMAR-GC approach accounting for the relationships between individuals based on SNP genotypes. SNPs with associations surpassing a statistical threshold of 5 x 10-5 were identified on BTA1 and 23.