The influence of the Jurassic hydrothermal activity on the interpretation of fission track (FT) data from the southern Upper Rhine Graben (URG) is elaborated by means of new zircon FT analyses on samples with known U/Pb crystallisation ages. Zircon FT central ages display a wide spectrum from 162 ± 14 Ma to 247 ± 22 Ma. The combination of the U/Pb ages, independent geologic evidence (such as Mesozoic subsidence history, timing of hydrothermal activity, and apatite FT ages) and the zircon FT data unambigously indicate a Jurassic thermal overprint in the investigated area. It is suggested that circulating hydrothermal fluids with temperatures in the order of 200-250 °C were responsible for the observed thermal anomaly. The Jurassic hydrothermal fluid migration appears to have been related to a heating event on a regional scale. Inferences from FT analyses related to burial or denudation history have to take into account how such hydrothermal events affect the FT system, including a changing geothermal gradient with time.