Tracks created by fission events in ceramics are randomly-oriented, linear radiation-damage regions about 10 to 25 μm in length but only several nm in diameter. In the absence of a method to observe the entire length of a latent, unetched track, the details of the structure and the process of the thermal-annealing of tracks have remained elusive, despite their importance to fission track thermochronology and radiation damage studies in nuclear materials. Here, we have used a novel sample preparation technique, together with advanced transmission electron microscopy (TEM), to successfully image the entire length and in situ thermal annealing of latent tracks created by 80 MeV Xe ions implanted in apatite. Track annealing significantly increases as the track diameter decreases along the ion trajectory from an initial diameter of 8.9 nm to ~ 1.5 nm at the end of the track (total track length ~ 8.1 μm). For the first time, the initial, rapid reduction in etched length during isothermal annealing can be essentially explained by the rapid annealing of the sections of the track with smaller diameters, as observed directly by TEM.Highlights► The entire length of unetched fission tracks was observed for the first time. ► The track diameter decreases along the fission fragment path. ► Track annealing significantly increases as the track diameter decreases. ► We are also able to measure the deviation angle from the original ion trajectory.