Although total sleep deprivation is frequently used in sleep research, the techniques used such as gentle handling are labor consuming and not standardized (and boring). In order to minimize these limitations, we developed a fully automated setup, which can be used for total sleep deprivation. A shortfall of individually adjustable thresholds of electromyogram (EMG) signals from sleep deprived animals was used online to switch running wheels incorporated into the home cages. Randomized direction of rotations, adaptable rotational speed and automatic deactivation of the running wheels during quiet waking of the animals provided robust and standardized sleep deprivation without increased stress, when compared to gentle handling. The setup can easily be introduced to a variety of home cages and is individually adaptable to each animal to be sleep deprived.