Passive implanted transponders (PIT tags) are currently widely use for identification of individuals in animal studies, and have successfully replaced most of the older marking methods. The advantage of this technique is an automatic registration of animal’s presence and storage of collected data. However, the main limitation of the automatic systems is high power consumption. Thus, to reduce the energy loss, energy-efficient motion detectors were applied. Newly implemented detectors turn on the power supply only when initiated by animal presence. Combination of transponder readers with camera-traps was used in order to estimate the proportion of marked and unmarked individuals in the population. In addition, this design enables application of capture-mark-recapture (CMR) statistical models. In comparison with traditional methods, the new technique is by far more cost-effective and is particularly suitable for long-term data collection. To demonstrate the usefulness of Automatic Transponder Readers, we present data on activity, movement and mortality of small and medium-sized mammals (mice, voles, dormice, weasels and martens).