Objective It was the objective of this study to describe and compare antimicrobial resistance in clinical and non-clinical E. coli from different cattle populations. Material and methods For this, the minimum inhibitory concentrations (MIC) of antimicrobials against clinical and non-clinical E. coli isolates from dairy cows, beef cattle, veal calves and other calves were analyzed. The MIC examinations were performed in the framework of a monitoring program for clinical isolates from animals in Germany (GE RM -Vet) and as part of the national zoonosis monitoring between 2009 and 2019 using broth microdilution. The MIC were evaluated based on the epidemiological cut off values provided by the European Centre for Antimicrobial Susceptibility Testing (EUCAST). Results A total of 5127 isolates was included in the analysis. The highest resistance rates were observed in isolates from calves with diarrhea, followed by non-clinical isolates from cattle slaughtered at an age under 1 year. The lowest resistance rates were encountered in E. coli from bulk tank milk of dairy herds and from beef cattle. Resistance rates of isolates from cases of mastitis were higher than of non-clinical isolates from bulk tank milk, but lower than the rates observed in calves. Conclusion and clinical relevance Resistance rates to the critically important antimicrobials fluoroquinolones and 3rd generation cephalosporins were high in isolates from mastitis samples and in isolates from calves with diarrhea. This may be linked to the high use of these substances in dairy cows and the feeding of wastemilk from treated cows to calves, exposing the latter to drug residues and resistant bacteria from the milk. The use of these substances has to be reduced to a minimum in order to avoid further spread of this kind of resistance in the cattle population.