Monitoring the movements of fish enables management decisions to be based on the ecological requirements of the species in question. PIT tags are a cost effective, long-term method of tracking large numbers of fish. As this technology has improved, the size of PIT tags has decreased, enabling smaller species, and younger fish to be tagged and tracked. There is limited information available on the possible effects that these tags have on the survival rates and subsequent health of small fish. Swimming performance is a physiological measure that is easy to quantify in the lab and directly relates to an individual fishes health. We used swimming performance to assess the effect of microPIT tags (8.4 mm) on five small-bodied, and juveniles of five large growing native Australian fish species. In an initial trial to assess suitability for microPIT tagging, two of the small-bodied species had high mortality and were categorised as unsuitable for tagging. Sample sizes were increased for the remaining eight species to quantify potential effects of microPIT tags on swimming performance. For these eight species we found no significant effects of microPIT tags on their swimming performance.