We evaluated the effect of 12-mm passive integrated transponder (PIT) tag implantation on age-0 brown trout Salmo trutta. The effects of implantation method (i.e. surgical incision or injection) and individual tagger on survival, tag retention and growth were assessed during a 60-day hatchery experiment. Two size classes of fish (total length) were considered: small (50–55 mm) and large (56–63 mm). For fish ≤ 55 mm, survival rate at 60 days was lower for tagged than for control fish (80.7 vs 91.2%, respectively), varied between taggers, but was not affected by the implantation method. For this size class injection resulted in a higher retention rate than surgical implantation (89.4 vs 69.4%, respectively); tag retention also varied among the individual taggers. The growth in length and weight of fish from this class was significantly impaired by tagging at 30 and 60 days (e.g. mean ± SD length at 60 days = 76.5 ± 8.4 mm for tagged fish vs 81.2 ± 7.9 mm for control), and individual specific growth rates (SGR) of tagged fish differed between taggers. In contrast, for larger fish (>55 mm), neither implantation method nor tagger affected survival (mean = 93.2%), tag retention (mean = 86.6%), and growth rate (mean ± SD specific growth rate = 1.07 ± 0.48% during the first 30 days). A slight slowdown in growth (length) appeared within 30 days post-tagging but was compensated at 60 days. Results suggest that implanting 12-mm PIT tags in salmonids smaller than 55 mm (TL), by different taggers and using either surgery or injection, may have significant effects on survival, tag retention, and growth.