International conventions dictate reliable identification of various reptile species that are subject to intensive trade targeting and habitat destruction. As a rule, tortoises with a minimal plastron length of 100 mm are fitted with a microchip transponder. The development of new generations of transponders, however, may offer the possibility to identify smaller individuals. This study evaluated the use of microchip transponders in juvenile Hermann's tortoises, Testudo hermanni, by using two groups of 30 captive-bred tortoises. Microchip transponders were implanted in the first group of tortoises, and the second group served as a control group. During a 10 month observation period, including 2 months of hibernation, both groups were evaluated for short- as well as mid-term effects of microchip implantation, and readability of the microchips was checked twice a week. Body weight and plastron length were determined twice a week to compare growth and weight curves between both groups. Radiographs were obtained from all animals immediately after microchip implantation, 4 wk later, and at the end of the observation period. In addition, applicability and readability of the marking method were evaluated in 130 tortoises (family Testudinidae) and 73 turtles (family Emydidae) with a plastron length exceeding 100 mm. Besides overall uncomplicated application and excellent readability, our results provide a solid basis for the assumption that the use of microchip transponders does not result in negative behavioral or physical effects and that they are safe to use in juvenile Hermann's tortoises, allowing at least mid-term identification of tagged individuals.