We compared detection efficiency for three lengths (12, 23 and 32 mm) of half-duplex (HDX) passive integrated transponder (PIT) tags for both manual tracking and fixed array applications. In a stream we used a wand-type manual tracking antenna and determined that detection efficiency was considerably influenced by tag size (i.e., 20% for 12 mm, 43% for 23 mm, and 81% for 32 mm) and water depth. Vertical and horizontal read range also varied among tag sizes (lower for smaller tags) and orientation (12-mm and 23-mm tags oriented perpendicularly failed to read in the horizontal test). Using a fixed PIT array, we also compared the detection efficiency of the same three sizes of PIT tags in Shorthead Redhorse Moxostoma macrolepidotum released into a fishway. Again, detection efficiency increased with tag size: 12 mm = 55.8 ± 9.2% (mean ± SE), 23 mm = 91.0 ± 1.8%, and 32 mm = 97.0 ± 1.5%. When using PIT telemetry on smaller fish species and/or life stages, we suggest that researchers consider the tag size, as the diminished detection efficiency of 12-mm tags could introduce a bias and impede the ability to address some research questions.