The brain is a massively interconnected network of specialized circuits. Even primary sensory areas, once thought to support relatively simple, feed-forward processing, are now known to be parts of complex feedback circuits. All brain functions depend on millisecond timescale interactions across these brain networks. Current approaches cannot measure or manipulate such large-scale interactions. Here we demonstrate that polymer-based, penetrating, micro-electrode arrays can provide high quality neural recordings from awake, behaving animals over periods of months. Our results indicate that polymer electrodes are a viable substrate for the development of systems that can record from thousands of channels across months to years. This is our first step towards developing a 1000+ electrode system capable of providing high-quality, long-term neural recordings.