A laboratory study was conducted to assess the effect of PIT tagging on survival and growth of young-of-the-year brown trout (Salmo trutta) and evaluate PIT tag loss as a function of body size at tagging. Transponders (11.5 mm long and 2.1 mm in diameter) were injected into the peritoneal cavity of fish ranging from 41 to 70 mm fork length (FL) using hypodermic needles. A total of 145 tagged fish and 136 control fish of similar size were reared over 4 weeks. Logistic regressions show that survival rate reached 95% for fish ≥52 mm FL at tagging (with a tag retention rate >70%), and 99% for fish ≥57 mm FL (tag retention rate >80%). No significant effect of tagging on growth (fork length and weight) was detected at the end of the experiment. The specific growth rate varied markedly among PIT-tagged fish regardless of fork length, weight or tag-to-body-weight ratio at tagging. Results suggest that juvenile brown trout larger than 57 mm FL (tag-to-body weight ratio in water <3.4%) can be marked by injection of 11.5 mm PIT into the peritoneal cavity with negligible effects on survival and growth, but this leads to a relatively high tag rejection rate (up to 20%).