Due to renewed interest in specialty cheeses, small-scale artisan and farmstead producers are manufacturing numerous varieties of cheese, including those that present higher risk such as surface-ripened soft cheeses, often using raw milk. The presence of pathogenic bacteria in raw milk on large scale dairy farms is well documented as the dairy farm itself can serve as a reservoir. To assess the risks associated with the use of raw milk in the manufacture of small-scale artisan cheese we evaluated overall milk quality and prevalence of four target pathogens (Listeria monocytogenes, Staphylococcus aureus, Salmonella spp., and Escherichia coli O157:H7) in raw milk from 11 farmstead cheese operations in Vermont. Although overall incidence was low in comparison to other surveys, variation from farm to farm, independent of species, indicates that some operations practice strict hygienic controls and that additional effort is needed on others. Our data also suggest that if present, pathogen population levels in raw milk are extremely low. Although these pathogens are readily inactivated by pasteurization, pasteurized milk and milk products, including soft cheese, have been implicated in major outbreaks of L. monocytogenes infection as the result of post-processing environmental contamination. U.S. Standards of Identity permit the manufacture of these and other cheeses from raw milk, provided they are aged for a minimum of 60 days typically at a temperature no less than 35°F (1.67°C) to provide safety. Of particular concern are the surface-mold-ripened soft cheeses due to the growth potential during aging and refrigerated holding following increases in pH. In a study on the growth potential of L. monocytogenes introduced as post process contaminants on surface-mold-ripened cheeses we demonstrate that holding cheese in compliance with U.S. Federal regulations supports pathogen growth from very low levels regardless of the whether the milk used was raw or pasteurized. Moreover, the 60 day aging rule encourages extended holding which could inadvertently contribute to risk. It is clear that the safety of cheeses within this category must be achieved through control strategies other than pasteurization or aging. Effective environmental monitoring and control of Listeria spp. within processing plants, including farmstead cheese operations, is considered paramount in reducing cross contamination of ready-to-eat foods. To assess the incidence and ecology of Listeria spp. in farmstead cheese processing environments we conducted environmental sampling in 9 different cheesemaking facilities over a 10-week period while comparing three detection/isolation protocols. Results indicate that the use of detection/isolation methods incorporating dual primary enrichment with a repair step allowing for the recovery of injured Listeria enhances detection of Listeria spp., including L. monocytogenes, and that the addition of PCR increases sensitivity of detection while greatly reducing time to results. Our data indicate that the extent of farmstead cheese plant contamination with Listeria spp., notably L. monocytogenes, is comparatively low for dairy processing plants, especially those with contiguous farms and aids in the identification of control points for use in designing more effective control and monitoring programs. Overall the studies contained herein fill data gaps in the literature considering the threat of emerging pathogens in raw milk intended for farmstead cheesemaking, as well as the incidence and distribution of Listeria spp., including molecular subtypes, in small farmstead cheese processing environments over time. These data will help inform risk assessments which evaluate the microbiological safety of artisan cheeses, particularly those manufactured on farms.