Electrochemical discharge machining (ECDM) involves the electrolytic formation of a gas film at a tool electrode with high current density discharges and Joule heating for local material heating and removal. The ECDM process is ideally suited for low density glass through-hole machining for applications such as fluidic interconnection. In this paper, we describe a simple and robust ECDM cell arrangement and present optimum conditions for rapid and reproducible through-hole machining in both 500 µm thick and fragile 180 µm thin borosilicate glass substrates. Both anodic and cathodic methods were evaluated and the results offer additional insight into the complex and polarity-dependent mechanisms involved in the ECDM process. The anodic process produces unique spherical cavity microstructures, presenting a new capability for glass microfabrication.