Johne’s disease (JD), caused by Mycobacterium avium ssp. paratuberculosis (MAP), affects approximately 70% of all US dairies. To determine if JD prevalence on PA organic dairy farms is different than that of conventional dairy farms; to identify differences in management practices between organic and conventional farms; and to identify risk factors associated with a higher prevalence of JD. Fifty PA dairy farms (26 certified organic, 24 conventional) participating in DHIA testing were included. Individual milk samples were tested for MAP antibodies via ELISA. Information regarding management practices was gathered during a farm visit. Univariable statistical comparisons were made by use of logistic and linear regression. Multivariable analysis was employed to look for risk factors and associations. A total of 2,739 cows were included in the study. Organic herds had a median of 39 lactating cows (range, 20–211 cows); while conventional herds had a median of 58 lactating cows (range, 20–114 cows) (P = 0.02). Average daily milk production was significantly higher in the conventional group (mean, 32.3 kg/d) versus the organic group (mean, 22.3 kg/d) (P = 0.05). Prevalence between herd types was not statistically different with 13/26 (50%) positive organic herds versus 14/24 (58%) positive conventional herds (P = 0.16). Among positive herds, the proportion of JD+ cows was higher (though not statistically different) for organic herds (2.3%) versus conventional herds (1.6%) (P = 0.24). Risk factors associated with JD+ on organic farms included: lack of routine vaccination, sharing of pasture and water source between adult cows and replacement heifers, and use of nurse cows. Risk factors associated with JD+ on conventional farms included: purchasing of animals, sharing of pasture and water source between adult cows and replacement heifers, feeding of whole milk to calves, and use of group maternity pens. The prevalence of JD on PA organic farms is no different than that of conventional farms matched by size. Although differences in management practices were identified between herd types, these differences did not have a significant effect on JD prevalence.