This study examines the utility of Passive Integrated Transponder (PIT) tagging system in fingerlings of gilthead seabream, Sparus auratus L. Two different body positions (abdominal, dorsal) and four weight classes (2–3 g, 3–4 g, 4–5 g, 5–8 g) were tested in three experiments. Tag loss rate, as well as its effect on growth and mortality rates, was determined. Times of handling and healing were also assessed. Fish tagged in the abdominal cavity showed a significantly lower tag loss rate (14%) than those given dorsal muscle implants (40%). No differences were found in growth within experiment between tagged and untagged fish, their final mean weight ranging between 6–39 g and 6–38 g, respectively. There was no difference in mortality between tagged and untagged fish at any position (0–3.4% and 0–2.1%, respectively). Fish smaller than 3 g suffered significantly higher mortality (14.3%), indicating that the PIT tags are not suitable for very small individuals. PIT retention rate was 100% above 4 g, irrespective of the personal expertise in tagging. Mean tag application time was 19 s per fish. Mean wound healing time was close to 20 days. Hence, these results showed that PIT tagging of gilthead seabream above 3 g is feasible because it does not affect growth or mortality.