Micro EDM using conventional pulse generators such as the RC type or transistor type with water as the dielectric fluid suffers from poor accuracy of machined structures due to electrolytic corrosion. In this study, a new high frequency bipolar pulse generator for micro EDM in water was developed in order to prevent electrolytic corrosion. The new pulse generator produced a high frequency bipolar pulse possessing a positive pulse duration of several hundred nanoseconds with a high repetition rate provided to the machining gap. Discharge characteristics of micro EDM using the new pulse generator were investigated. Machining characteristics were also investigated according to machining conditions such as the repetition rate, positive voltage, capacitance and resistivity. Using the new pulse generator, micro holes without electrolytic corrosion were successfully fabricated in deionized water and tap water. Machining time, tool wear and clearance using the new pulse generator in deionized water decreased compared with those using the RC circuit in kerosene.