The success of high-density electrode arrays for use in neural prostheses depends on efficient impedance monitoring and fault detection. Conventional methods of impedance testing and fault detection are time consuming and not always suited for in vivo assessment of high-density electrode arrays. Additionally, the ability to evaluate impedances and faults such as open and short circuits, both in vitro and in vivo, are important to ensure safe and effective stimulation. In this work we describe an automated system for the rapid evaluation of high-density electrode arrays. The system uses a current pulse similar to that used to stimulate neural tissue and measures the voltage across the electrode in order to calculate the impedance. The switching of the system was validated by emulating a high-density electrode array using light-emitting diodes and a resistor-capacitor network. The system was tested in vitro and in vivo using a range of commercially available and in-house developed electrode arrays. The system accurately identified faults in an 84-electrode array in less than 20 s and reliably measured impedances up to 110 kΩ using a 200 µA, 250 µs per phase current pulse. This system has direct application for screening high-density electrode arrays in both clinical and experimental settings.