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Thumping the back foot is a natural reaction among rabbits to danger that they have smelt, heard or seen.
Rabbits stand on all four feet, sometimes in a tip-toe position, with their ears alert, then lift their rear feet and thump to warn other rabbits in the warren that there is danger. Some rabbits will thump one foot on the ground, some will thump both hind feet at the same time. Rabbits aren't very vocal so thumping is an important way of communicating. They may remain in the thumping posture until convinced that the danger is gone. The length of time between thumps can vary from a few seconds to a couple of minutes and may last an extended period of time (even an hour or more).
Rabbits may perceive 'danger' from many different novel things: it could be a wood fire in the home, a lit cigarette, rapid or unpredictable movement, the shadow of a bird flying by, or a cat walking past. A rabbit who is exhibiting continual thumping can die from extreme stress and should be removed from the perceived 'danger' immediately, and reassured and comforted.
Some rabbits may also display thumping as a show of disapproval. This may relate to different situations which can be identified by observing the circumstances where this behaviour is displayed. There is no need to stop rabbits thumping unless it becomes excessive and then modifying the environment is the best approach. Never punish a rabbit for undesirable behaviour.