Studying the movements of organisms that live underground for at least a portion of their life history is challenging, given the state of current technology. Passive integrated transponders (PIT tags) provide a way to individually identify and, more recently, study the movement of smaller animals, including those that make subterranean movements. However, there are widespread assumptions of the use of PIT tags that remain problematic. We tested the effects of PIT-tag implantation on growth and survival, along with the effects of electromagnetic fields for reading PIT tags on behavior, of the smallest salamander that has been PIT-tagged: the Red-Backed Salamander. We found no effect of PIT tags on growth or survival. Using a mesocosm experiment, we also found that electromagnetic effects associated with reading PIT tags, had no effect on salamander behavior. Further, we describe a novel PIT antenna and soil mesocosm experimental arena for studying belowground movements of woodland salamanders. Collectively, these studies suggest that the use of PIT tags do not influence the growth, survival, or behavior of Red-Backed Salamanders. Given the challenges of studying salamanders that live underground and the impending changes in climate and landscapes, this research suggests that PIT tags remain a viable tool for studying the movement ecology of salamanders under global change.