The damage formed by 1.25 MeV, self‐ions in Si at liquid nitrogen temperature was studied. A dominant feature of the damage for moderate ion fluences is the presence of isolated amorphous regions over the range of the ions. The microstructure of this damage is detailed and formation mechanisms discussed. The amorphous regions are shown to give rise to strain in the surrounding crystal lattice which varies with ion dose in a complicated manner. The annealing behavior of the damage was studied and two distinct, low‐temperature stages observed. Different mechanisms are shown to be responsible for each stage including a transient mechanism at 300 °C initiated by the release of defects from damage clusters, and enhanced crystallization of amorphous Si at 400 °C due to lattice stress.