Microglial cells are the innate immune cells of the central nervous system. In the healthy adult brain “resting” ramified microglia continuously palpate their environment to monitor the integrity of and to react to any disturbance of brain homeostasis. During injury, inflammation, and in the course of neurodegenerative diseases microglia become activated, proliferate, and release a plethora of cytokines as well as reactive oxygen species. In addition to their well known role in disease, it has become increasingly clear that “resting” microglia also contribute to normal brain physiology, both during postnatal development and in the mature adult brain. Functional in vivo imaging of microglia first of all captures the morphological changes accompanying microglial transition between “resting” and activated states. In addition, intracellular Ca2+ homeostasis of microglia is believed to be altered between the two states [1–3]. So far, however, microglial Ca2+ signaling was predominantly studied in reduced preparations like brain slices or cell cultures, in which microglia are found in a rather activated state. In this chapter we describe a technique for studying microglial Ca2+ signaling in vivo. Furthermore, we discuss a new approach for visualization of morphological dynamics of microglial cells in vivo at high resolution. This approach utilizes a lectin-based staining technique and is applicable to any deliberate mouse strain at any developmental stage.