Dairy farm hygiene audits were undertaken at 24 farms during summer and winter and the results compared with transformed bacterial indicator levels in raw milk samples collected during each audit. The bacterial indicators measured were total viable counts, Escherichia coli, coliforms, Bacillus spp., Bifidobacteria spp., and Pseudomonas spp. The results of initial comparisons using Pearson product-moment correlation coefficients showed presumptive relationships between some bacterial groups and the subjective quantitative audit scores. When investigated further using linear regression, the presumptive relationships were found to be influenced by external factors. Possible reasons for the low correlations between on-farm hygiene and bacterial indicator counts in raw milk were further investigated. Measurements of the uncertainty associated with the bacteriological results were undertaken and revealed geometric relative standard deviations that ranged from 0.019 to 1.05. Toward the higher end of this scale, the uncertainty associated with the laboratory estimations of bacterial numbers may have been large enough to blur hygiene score-marker bacteria relationships. The samples obtained from on-farm raw milk storage tanks were representative of the whole tank contents and not a significant source of error. Although total bacterial counts are widely acknowledged by the milk industry as not always giving a true measure of on-farm hygiene during milking, we were unable to find any marker bacteria that showed consistently higher correlations and were thus better suited as indicators of on-farm hygiene.