Several variations of microelectrode arrays are used to record and stimulate intracortical neuronal activity. Bypassing the immune response to maintain a stable recording interface remains a challenge. Companies and researchers are continuously altering the material compositions and geometries of the arrays in order to discover a combination that allows for a chronic and stable electrode-tissue interface. From this interface, they wish to obtain consistent quality recordings and a stable, low impedance pathway for charge injection over extended periods of time. Despite numerous efforts, no microelectrode array design has managed to evade the host immune response and remain fully functional. This study is an initial effort comparing several microelectrode arrays with fundamentally different configurations for use in an implantable epilepsy prosthesis. Specifically, NeuroNexus (Michigan) probes, Cyberkinetics (Utah) Silicon and Iridium Oxide arrays, ceramic-based thin-film microelectrode arrays (Drexel), and Tucker-Davis Technologies (TDT) microwire arrays are evaluated over a 31-day period in an animal model. Microelectrodes are compared in implanted rats through impedance, charge capacity, signal-to-noise ratio, recording stability, and elicited immune response. Results suggest significant variability within and between microelectrode types with no clear superior array. Some applications for the microelectrode arrays are suggested based on data collected throughout the longitudinal study. Additionally, specific limitations of assaying biological phenomena and comparing fundamentally different microelectrode arrays in a highly variable system are discussed with suggestions on how to improve the reliability of observed results and steps needed to develop a more standardized microelectrode design.