<p>Conventional intravital microscopy has generally been limited to superficial brain areas such as the olfactory bulb, the neocortex, or the cerebellar cortex. <em>In vivo</em> optical microendoscopy uses gradient refractive index (GRIN) microlenses that can be inserted into tissue to image cells in deeper areas. This protocol describes <em>in vivo</em> microendoscopy of the mouse hippocampus. The general methodology can be applied to many deep brain regions and other areas of the body.</p>