The invention relates to an animal treatment system for treating an animal, for instance a teat of an animal, comprising supply means for supplying treatment fluid to an animal, which supply means can be coupled in fluid throughflow connection to a container for containing treatment fluid, wherein the animal treatment system comprises: - recording means for recording identification information on a container, and - a processor for receiving the identification information recorded by the recording means and, on the basis of the recorded identification information received and predefined criteria, controlling the supply means for the purpose of discharging or not discharging treatment fluid from a container. The invention also relates to a milking system for milking animals and a cleaning system for a milking system.