Automated calf feeding systems are growing in popularity across the United States, yet research identifying risk factors that influence calf health is limited. This ongoing study is investigating associations between farm management, environment and housing with calf health outcomes. Thirty-eight Midwestern dairy farms were visited approximately every 60 d for 18 mo. During each visit calves (n = 10,185) were scored by a single observer for health outcomes including attitude, secretions of the ears, eyes and nose, and cleanliness of the rear end as evidence of diarrhea (0 = normal, clean calf – 58.1% of the scores; 1 = moderate coverage of loose feces – 32.4%; 2 = significant coverage of watery fecal material – 9.4%). Risk factors for higher cleanliness score (diarrhea) were assessed using multilevel ordinal logistic regression. Variables in the analysis included pen size, group size and stocking density, farm’s colostrum management, and milk diet type, amount, formulation, and bacterial count. Non-significant variables were removed using backward elimination. Variable retention was set at P < 0.05. The association between season and cleanliness score was found to be highly significant. Odds ratios indicated that winter 2012–13 (0.78), spring 2013 (0.43), summer 2013 (0.54), fall 2013 (0.72), and spring 2014 (0.47) were all associated with reduced likelihood of diarrhea compared with winter 2013–14. Each liter increase in peak milk allowance was associated with an 11.6% decrease in odds of higher score or diarrhea (OR 0.88, P = 0.001). The number of days taken to reach peak milk allowance was also associated with higher score (OR = 1.02, P = 0.006). Increasing number of calves per group was associated with a small decrease in score or less diarrhea (OR = 0.99, P = 0.04). The magnitude of association observed for greater peak milk allowance suggests that feeding calves on a higher plane of nutrition, and reaching that plane earlier, may be beneficial in reducing observed diarrhea. This project is supported by Agriculture and Food Research Initiative competitive grant no. 2012-67021-19280 from the USDA National Institute of Food and Agriculture.