Resistant bacteria from food-producing animals may compromise the success of antibiotic treatment in animals and in humans. Therefore, the level of antibiotic resistance in bacteria from farm animals and its development over time needs to be monitored. In Switzerland, a monitoring program for antibiotic resistance is currently being developed. Pilot-monitoring programs were conducted in selected animal species in order to obtain current data on antibiotic resistance. The data on the prevalence of bacteria and antibiotic resistance in poultry were used to optimize the sampling plan. The influence of sampling more farms compared to sampling more animals per farm on the prevalence estimate for antibiotic resistance was analyzed by a Monte Carlo simulation model. Accounting for the costs for sample collection, transportation and laboratory analysis of the samples, the number of samples to be taken at the respective step in the production line was optimized. Optimization was defined as maximizing the precision of the prevalence estimate while minimizing the costs. The model will be expanded to other bacterial and animal species in the future.