Laser micromachining has been widely used for decades to fabricate the micro- and submicro-component structures. However, thermal and physical damages are crucial issues associated with the process. Underwater laser ablation has been developed as a damage-free micro-ablation technique. In this paper, a comparison of the conventional dry and underwater laser micromachining of silicon is presented. It shows that the heat affected zone (HAZ) can be reduced significantly in the underwater laser process, though the material removal rate is reduced due to the energy loss by the water layer. The effects of pulse frequency, traverse speed and laser energy on the obtained kerf width, HAZ and cut surface quality are also analyzed and discussed.