To track individuals in situ, over 12 million salmon and trout have been marked with passive integrated transponder (PIT) tags in the Columbia River Basin, USA. However, few studies have examined long term tag retention as well as tag effects on juvenile salmon and trout. We marked juvenile coho salmon Oncorhynchus kisutch (N = 207), steelhead (anadromous rainbow trout) O. mykiss (N = 221), cutthroat trout O. clarkii (N = 202) and bull trout Salvelinus confluentus (N = 180) with 12, 19, or 23 mm PIT tags and examined tag retention, survival, growth, and physiological performance over a six month period in a laboratory environment. PIT tag retention rates were high for coho salmon (100%), steelhead (95%), cutthroat trout (97%), and bull trout (99%), regardless of tag size. Survival was also high for coho (99%), steelhead (99%), cutthroat trout (97%), and bull trout (88%) and did not vary among tag sizes. Short term individual growth rates for coho salmon marked with 12 mm tags were significantly higher than those marked with 19 mm and 23 mm PIT tags. Likewise, steelhead trout individual growth rates were lower for fish marked with 23 mm PIT tags followed by 19 and 12 mm tags. Conversely, long-term growth rates were positive and not affected by tag size. There were no significant effects of tag size or marking on coho gill Na+, K+, -ATPase activity (µmol ADP x mg protein–1 h–1) and plasma osmolality (µmol kg–1) or bull trout hepatosomatic indices. Our study suggests that marking juvenile salmonids with PIT tags results in high retention with little effect upon their survival, growth, and important physiological indicators regardless of tag size in a laboratory environment.