Ca2+ mobilization in response to crosslinking of IgE bound to its high affinity receptor, FcεRI, on mast cells is central to immune allergic responses. Stimulated tyrosine phosphorylation caused by this crosslinking activates store-operated Ca2+ entry that results in sustained Ca2+ oscillations dependent on Rho family GTPases and phosphoinositide synthesis. Coupling of the endoplasmic reticulum (ER) Ca2+ sensor, STIM1, to the Ca2+-selective channel, Orai1, is regulated by these elements and depends on membrane organization, both at the plasma membrane and at the ER. Mitochondria also contribute to the regulation of Ca2+ mobilization, and we describe recent evidence that the ER membrane protein VAP plays a significant role in the coupling between ER and mitochondria in this process. In addition to granule exocytosis, Ca2+ mobilization in these cells also contributes to stimulated outward trafficking of recycling endosomes and to antigen-stimulated chemotaxis, and it is pathologically regulated by protozoan parasitic invasion.