Use of antimicrobials for food-producing animals is a major public concern due to the risk of antimicrobial resistance. Although dairy production has a relatively low usage of antimicrobials, the potential for further reduction should be explored. The objective of the study was to estimate the current differences in antimicrobial use in Danish organic and conventional dairy herds and to describe the differences between them. Based on data from three different sources, 2604 herds (306 organic and 2298 conventional) were identified for the study. These herds had been either organic or conventional for the entire period from 2015 to 2018. Antimicrobial use was calculated as the treatment incidence in Animal Daily Doses (ADDs)/100 animals/day for three age groups: adult cattle, young stock and calves. For adult cattle, the ratio of median treatment incidence between conventional and organic production ranged from 2.8 : 1 to 3.4 : 1, depending on the specific year. For cows, 25% of the organic herds had a higher treatment incidence than the 25% of conventional herds with the lowest treatment incidence. Antimicrobial use for young stock was low and at a similar level in both the organic and conventional production systems. For calves, the median treatment incidence was 1.2 times higher in conventional herds and 1.6 times higher for the 75th percentile. Analyses of treatment incidence in adult cattle showed an overall decrease from 2015 to 2018 in both organic and conventional herds. The decrease was greater for the conventional herds (0.12 ADD/100 animals/day) compared to the organic herds (0.04 ADD/100 animals/day) over the 4-year period. In addition, herd size was an important risk factor for treatment incidence in conventional herds, increasing by 0.07 ADD/100 animals/day per 100 cows, whereas herd size had a minor influence on the treatment incidence in organic herds. The results of this study demonstrate the large variation in antimicrobial use within both organic and conventional herds, suggesting that further reduction is possible. Furthermore, herd size appears to be a risk factor in conventional herds but not in organic herds – an aspect that should be studied in more detail.