A subjective cow cleanliness scoring system was validated and used to assess the cleanliness score of dairy cows at different times in the year. A longitudinal study followed a number of farms from summer to winter, and a larger, cross-sectional study assessed a greater number of farms during the housed winter period. The scoring system was demonstrated to be both a repeatable and practical technique to use on-farm and showed that cows become dirtier in the transition from summer grazing to winter housing. Although farming system (organic or conventional) had no effect on cow cleanliness when cows were at grass, when housed in the winter, organic cows were significantly more likely to be cleaner. There was a link between cow cleanliness scores and milk quality, with herds having lower bulk tank somatic cell counts (BTSCC) tending to have a lower (cleaner) median cow cleanliness score; with this relationship strongest for the organic herds. There was no significant link between cleanliness score and Bactoscan (BS) count or clinical mastitis incidence. No major mastitis pathogens were cultured from bulk tank milk samples from the quartile of herds with the cleanest cows in contrast to the quartile of herds with the dirtiest cows, where significant mastitis pathogens were cultured. Based on this study, all farms, especially organic systems, should attempt to keep cows clean as part of subclinical mastitis control.