All dairy farms authorized to produce and sell raw milk in a province of Northern Italy were investigated to determine the presence of Campylobacter spp., verocytotoxin-producing Escherichia coli (VTEC), Listeria monocytogenes, and Salmonella spp. in in-line milk filters and to assess their association with suspected risk factors on farms. A logistic regression model was used to analyze data collected describing the characteristics and management practices of 27 farms and the microbiological status of 378 in-line milk filters by both culture-based and molecular methods. Thermotolerant Campylobacter, VTEC, and L. monocytogenes were detected in 24 (6.45%), 32 (8.4%), and 2 (0.5%) samples, respectively. No Salmonella spp. were detected. For risk analysis, data of L. monocytogenes and Salmonella spp. were not included in the model because of the low prevalence or absence of these organisms. The univariate analysis disclosed that the presence of VTEC and/or Campylobacter spp. in milk filters was associated with lack of cleanliness of bedding, water trough, and feed trough; nonevaluation of water hardness; lack of cleanliness of milk tank; and nonapplication of forestripping. After multivariate analysis, an association was observed with inadequate cleanliness of bedding and milk tank and the nonapplication of forestripping. PCR analysis of milk filters was a rapid and sensitive method for the microbiological evaluation of herd contamination status and should be included among the registration requirements for the authorization to produce and sell raw milk. Specific control actions must be incorporated into the farmer's daily practices to ensure the low-risk production of raw milk.