Infectious diseases in dairy cattle are of significant concern to dairy industries because of their huge impact on animal health, milk production, and economics. Mycobacterium avium subsp. paratuberculosis (MAP)is a pathogenic bacterium that causes Johne's disease, one of the important endemic infectious diseases in dairy cattle. Contamination of bulk tank milk with MAP can occur through direct shedding into milk by infected cows (internal route), fecal contamination (fecal route), or introduction of soil and water containing MAP (environmental route). Humans can be exposed to MAP via raw milk consumption; additionally, there are reports of MAP survival in milk after pasteurization. The risk of human consumption is particularly important due to an association between MAP and human Crohn's disease. In the current study, we used a probabilistic modeling framework to predict the level of MAP contamination per liter in the bulk tank milk and weigh the relative importance of each contamination route. Our model focused on several different infection statuses and the contribution of each group to environmental and fecal contamination, in addition to internal route shedding. We assessed the influence of common hygiene practices, such as washing of udders before milking and the use of milk filters, on the concentration of MAP in bulk tank milk. We extracted parameters and their distributions from national surveys and thorough literature search. Our baseline model comprising all hygiene practices provided an average estimate of 0.76 log CFU/L for the final concentration of MAP in bulk tank milk, with a maximum of 6.70 log CFU/L and a minimum of 0.04 log CFU/L depending on herd size and the ratio of infection statuses. Results from sensitivity analyses indicated that the average fecal contamination showed the greatest impact on the final MAP concentration per liter in bulk tank milk, followed by herd size and washing efficiency. This study emphasized that good hygiene practices are crucial for maintaining the quality of raw milk in an endemically-infected dairy herd.