In order to explain the relatively easy laser-induced desorption of hydrogen implanted in silicon, and particularly the lower temperature needed for desorption at higher implantation energy, the microstructural modifications produced by laser pulses were studied by means of transmission electron microscopy. The structural damage, such as defect clusters and hydrogen gas bubbles was observed. In the case of low dose implantation (H/Si ≤ 15&), most of the bubbles were produced during laser annealing rather than during implantation. This bubble formation in the course of desorption explains the higher temperature needed. When blisters are already present on the as-implanted surface, desorption starts at a lower temperature.