The primary objective of this study was to identify compost bedding characteristics associated with mastitis epidemiologic indexes, cow cleanliness, and concentration of selected bacterial populations found in bulk tank milk. Secondary objectives were to monitor the occurrence of environmental mastitis outbreaks, and to describe the profile of pathogens isolated from mastitis cases of cows housed in the CBP system. Three dairies were visited monthly during 1 year. On each visit day, milk samples were collected from the bulk tank and from a sample of mammary quarters for microbiological examination. Milk samples were collected from all cases of clinical mastitis. Flank, leg, udder, and teat cleanliness were assessed using a score chart based on a 4-point scale (1=clean to 4=very dirty). Bedding samples were collected to estimate concentrations of total bacteria, streptococci, and coliforms, moisture, organic matter, carbon–nitrogen ratio, pH, and density. Mixed models were used to identify factors associated with incidence and prevalence of mastitis, and cow cleanliness. Except for farm A, on which contagious pathogens caused most cases, Escherichia coli, coagulase-negative staphylococci, and environmental streptococci were the most frequent pathogens isolated from clinical mastitis cases. Corynebacterium bovis was the most frequent pathogen isolated from subclinical cases of farms B (17.6) and C (26.0%). Environmental pathogens were isolated from 17.2%, 10.1%, and 14.8% of all subclinical cases of farms, A, B, and C, respectively. No outbreaks of environmental mastitis were observed during the course of the study. Bedding moisture, carbon–nitrogen ratio, pH, and dry density were unconditionally associated with the incidence of environmental clinical mastitis. Nonetheless, bedding moisture remained as a sole predictor in the final model. The odds of a case of environmental clinical mastitis increased 5.7% for each one-unit increase in bedding moisture. The odds of a new case of subclinical mastitis, and of a cow having SCC ≥200,000cells/mL increased 32% and 16% for each one-unit increase in leg cleanliness score, respectively. Overall means for udder, teat, flank, and leg hygiene scores were less than 2.1 for all farms and did not vary among seasons of the year. Bedding wet density was positively associated with all cleanliness scores and bulk milk concentration of total bacteria. Results suggest that managing bedding to remain dry and loose will result in cleaner animals with decreased risk of mastitis.