Antimicrobial use is a commonly applied proxy for animal health and welfare impairment related to disease status in dairy herds. The objective of this study was to estimate the association between antimicrobial use and the results of systematic clinical examinations for metritis and mastitis. Data was collected from 109 Danish dairy herds over a 5-year period. Statistical analysis demonstrated that the results of vaginal examinations and California mastitis tests on fresh cows were poor predictors of antimicrobial use at the herd level and 52% of the variance in the clinical data could be explained by herd-level factors. The results could be explained by the concept of a treatment threshold within each herd. We suggest that antimicrobial use should be categorised as a decision made by the herd manager rather than an approximation of disease status in the herd.