Thumping of the back legs 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 everyone 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 their 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).
This "danger" could be a furnace, an electrical appliance turning on or a lit cigarette when they are not used to the smoke. "Danger" could be the shadow of a bird flying across the moon or a cat walking on the window sill chasing a shadow on the floor. A rabbit who is exhibiting continual thumping can die from fright and should be reassured and comforted as soon as possible.
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