The calcium ion is a fundamental second messenger that plays crucial roles in the pathophysiology of brain cells. In this chapter, we will focus on the measurement of calcium fluctuations as a reporter of cellular excitability of both neurons and glial cells in the intact central nervous system. We will first describe the methodological aspects of in vivo two-photon fluorescence calcium imaging and then review recent data highlighting the ways in which this technique is revolutionizing our understanding of brain circuits at the cellular level. Finally, we will discuss recent technical advancements that promise to open new horizons in the optical investigation of brain function in awake, behaving animals.