Temperature is important to desert reptiles as it affects many aspects of their lives, including their ability to digest food, avoid overheating, and conserve water. Climate change creates increased urgency to understand the thermal ecology of desert reptiles and to develop tools for advancing such efforts. For decades, biologists have measured reptile internal body temperatures (Tb) using fine-gauge thermocouples inserted into the cloaca. Recent studies demonstrate that new tools such as infrared pyrometry and thermography may offer non-invasive means to estimate internal Tb in small lizards. We investigated the efficacy of thermography to estimate internal Tb in hatchling desert tortoises (n=39) in a controlled laboratory setting as part of a larger headstart program. We exposed hatchlings to one of two experimental thermal gradients (~22–40 or 22–60 °C) for 3 hours and compared paired surface (thermal camera) and cloacal (thermocouple) temperatures under warming (0.5 h), elevated (2.5 h), and cooling (2.5 h) temperature conditions. We then compared surface and internal Tb of hatchlings during normal activity within their home enclosures.  We present findings from these analyses and additional observations that highlight limitations and strengths of thermography in juvenile tortoise research and conservation.