The objectives of this research were (1) to study different factors affecting milk total bacterial count (TBC) and (2) to estimate the economic value associated with TBC in Holstein dairy herds in Iran. The relationships between bulk tank TBC and farm management and economic factors were examined on 56 randomly selected intensive dairy farms. Herd management factors associated with bulk tank TBC were determined using mixed linear models. The median bulk tank TBC for the sample herds was 299 (range 81–1185) × 103 cfu/ml. The average economic premium opportunity from bulk tank TBC was US$ 1.32 per ton of milk ranging from US$ 0.02 per ton of milk for herds applying wet tissue procedures as teat cleaning material and washing the water troughs three times per day to US$ 5.20 per ton of milk for herds with dirty barns. Results showed that the following management factors were associated with low TBC and high economic value: frequency of cleaning water troughs, teat cleaning material, the frequency of milk delivery to the processor, bedding material, herd size, education level of workers, udder washing material, material of milking parlor wall, frequency of disinfection of the calving area, presence of veterinarian, water quality control, having a hospital pen and barn hygiene. In conclusion, our findings highlight the need to pay more attention to farm management issues, particularly farm hygiene practices to reduce milk TBC and so reduce the economic burden of TBC in dairy herds in Iran.