The intracellular free calcium concentration subserves complex signaling roles in brain. Calcium cations (Ca(2+)) regulate neuronal plasticity underlying learning and memory and neuronal survival. Homo- and heterocellular control of Ca(2+) homeostasis supports brain physiology maintaining neural integrity. Ca(2+) fluxes across the plasma membrane and between intracellular organelles and compartments integrate diverse cellular functions. A vast array of checkpoints controls Ca(2+), like G protein-coupled receptors, ion channels, Ca(2+) binding proteins, transcriptional networks, and ion exchangers, in both the plasma membrane and the membranes of mitochondria and endoplasmic reticulum. Interactions between Ca(2+) and reactive oxygen species signaling coordinate signaling, which can be either beneficial or detrimental. In neurodegenerative disorders, cellular Ca(2+)-regulating systems are compromised. Oxidative stress, perturbed energy metabolism, and alterations of disease-related proteins result in Ca(2+)-dependent synaptic dysfunction, impaired plasticity, and neuronal demise. We review Ca(2+) control processes relevant for physiological and pathophysiological conditions in brain tissue. Dysregulation of Ca(2+) is decisive for brain cell death and degeneration after ischemic stroke, long-term neurodegeneration in Alzheimer's disease, Parkinson's disease, Huntington's disease, inflammatory processes, such as in multiple sclerosis, epileptic sclerosis, and leucodystrophies. Understanding the underlying molecular processes is of critical importance for the development of novel therapeutic strategies to prevent neurodegeneration and confer neuroprotection.