Ion channeling and cross‐sectional transmission electron microscopy were used to study the extent and nature of Si ion implantation damage in epitaxial GaN layers at liquid nitrogen temperature. Results indicate that displacement damage produced by the implantation undergoes substantial dynamic annealing during implantation. As a result, at moderate implantation doses residual implantation damage consists of a dense network of secondary defects, such as clusters and loops, which are a consequence of incomplete annihilation of implantation‐produced defects. Amorphous layers can be produced, but the doses required are extremely high (≳1016 cm−2) and amorphization appears to ‘‘nucleate’’ at the surface.