As automated calf feeders become more widely adopted, there is a need for research on sanitation management. The objective was to identify factors associated with bacteria counts and log reduction (LR) as a result of circuit cleaning (CC) in milk/replacer samples collected from automated calf feeders (Förster Technik, Engen, Germany). It was hypothesized that increased cleaning is associated with low bacteria counts and increased LR. Six VA and 4 MN dairy farms (14 feeders) were visited weekly for 7 mo. Samples of milk/replacer were collected aseptically from each feeder, iced, and frozen at −5°C. For a 4-wk period, VA farms were instructed to collect and freeze samples immediately before and after CC. Samples were thawed and plated on Petrifilms to find log₁₀ aerobic plate count (APC) and log₁₀ coliform count (CCP). From a model of state, farm(state), LSM ± SE APC was 3.84 ± 0.26 and 5.02 ± 0.21 log₁₀ cfu/mL (P < 0.01), and CCP was 0.62 ± 0.47 and 2.89 ± 0.39 log₁₀ cfu/mL (P < 0.01) for MN and VA. The LSM by farm ranged from 3.30 to 5.51 log₁₀ cfu/mL APC and 0.07 to 3.82 log₁₀ cfu/mL CCP. The LR of APC (LRAPC) and CCP (LRCCP) after CC was 0.78 ± 0.82 and 0.67 ± 1.17 log₁₀ cfu/mL (mean ± SD). By regression, each log₁₀ increase in pre-CC APC and CCP increased LRAPC and LRCCP by 0.45 log₁₀ cfu/mL (P < 0.01). Farms with higher pre-CC APC and CCP cfu/mL performed more CC/wk and used more mL detergent/L water (P < 0.05). More mixer cleanings (MCHE)/d lowered pre-CC APC cfu/mL (P < 0.05), whereas use of silicon hoses increased pre-CC CCP cfu/mL (P = 0.04), and use of bleach decreased pre-CC CCP cfu/mL (P < 0.01). By stepwise regression with farm in the model, more days since last MCHE increased LRCCP (P < 0.01) within farm. Number of calves, milk L/d, and feeder visit frequency were not associated with LR of bacteria within farm. LR was more dramatic at high pre-CC bacteria, which was reduced by more MCHE/d and use of bleach.