The in vivo biocompatibility of pure sapphire and borosilicate glass (BSG) implanted onto the cerebral cortex was studied via magnetic resonance imaging (MRI) and histopathology. Each implant was embedded onto the cortical surface of an adult rat brain for a total of 28 days. Rats underwent surgery with and without implants, and rats with purposely damaged cortical implant sites were also studied. Each animal was imaged via MRI before surgery as well as 10 and 28 days after the surgery. Histopathological results of animals were obtained on the 28th day to determine the specific effect on neurons. Despite the fact that sapphire has been widely used in a variety of medical implants, both MRI and histopathological results indicate that pure sapphire is not biocompatible with the cerebral cortex. On the contrary, BSG implants appear to be biocompatible with the cortical surface.