Calcium ions exert their effects in part via interactions with a wide variety of intracellular calcium-binding proteins. One class of these proteins shares a common calcium-binding motif, the EF-hand. A consensus amino acid sequence for this motif has aided the identification of new members of this family of EF-hand proteins, which now has over 200 members. A few of these proteins are present in all cells, whereas the vast majority are expressed in a tissue-specific fashion. The physiological function of a few of these proteins is known to be achieved via a calcium-dependent interaction with other proteins, thereby regulating their activity. Some members, like parvalbumin, calbindin, and calretinin, proved to be useful neuronal markers for a variety of functional brain systems and their circuitries. Their major role is assumed to be buffering, transport of Ca2+, and regulation of various enzyme systems. Since cellular degeneration is accompanied by impaired Ca2+ homeostasis, a protective role for Ca(2+)-binding proteins in certain neuron populations has been postulated. Another protein family are the annexins, members of which interact with phospholipids and cellular membranes in a calcium-dependent manner. In some cases members of the annexin family were even found to interact with EF-hand proteins. Certain annexins have been suggested to be involved in anti-inflammatory response, inhibition of blood coagulation, membrane trafficking or cytoskeletal organization, but several of these functions have been questioned recently. The elucidation of the interactions and functions of the majority of these proteins remains a challenging task for the coming years.