Calcium plays a major role in normal functioning of the cells. Deregulation of calcium-mediated signaling has been implicated in many neurodegenerative diseases including Alzheimer’s disease. Studies in neurons and mice expressing Alzheimer’s disease-associated transgenes have shown that the expression of familial Alzheimer’s disease (FAD) mutants of presenilin (PS) and amyloid precursor protein (APP) alter calcium homeostasis and cause synaptic dysfunction and dendritic spine loss in neurons. Mechanistic studies have shown that FAD mutants of presenilin can affect the intracellular calcium levels by affecting the ER calcium stores. A function for presenilins as ER calcium leak channels has been established and studies show that presenilins affect ER calcium load through an effect on IP₃ receptors, ryanodine receptors, or SERCA pumps. Even in the absence of an active gamma-secretase complex, presenilins seem to affect calcium homeostasis suggesting that these two functions of presenilins are independent of each other. Studies using FAD mutants of APP have shown that unlike presenilins, FAD-APP do not affect calcium homeostasis in the absence of Aβ. Both Aβ and presenilins seem to affect calcium homeostasis at very early stages of disease development affecting the synaptic transmission and function prior to neuritic plaque development. Altered calcium signaling differentially regulates genes such as calcineurin, calmodulin kinase II, MAP kinase etc and induces protein modifications and neurite degeneration. Since functional synapses and synaptic transmission are fundamental processes in memory formation, alterations in these processes can lead to neuronal dysfunction and memory deficit as seen in Alzheimer’s disease. This chapter gives an overview of calcium signaling in different systems, specifically neurons, the functioning of pre- and post-synaptic signaling, and how their deregulation influences pathology development in Alzheimer’s disease.