The emerging significance of calcium stores in neuronal plasticity and the assumed involvement of dendritic spines in long-term plastic properties of neurons have led us to examine the presence and possible regulation of calcium stores in dendritic spines. Immunohistochemical staining for ryanodine receptors was found in dendritic spines of cultured hippocampal neurons. Confocal microscopic imaging of calcium transients in dendritic spines of these neurons in response to caffeine allowed us to demonstrate an independent and unique calcium store in spines. The response to caffeine was blocked by thapsigargin and ryanodine, and maintained in calcium-free medium. The calcium stores were depleted faster in the spines than the dendrites. Furthermore, when calcium was released from stores under calcium-free conditions, and diffused passively between the spine and the dendrite, the length of the spine neck determined the degree of spine independence. Finally, the caffeine-sensitive ryanodine receptor-linked calcium store was instrumental in regulating the response of neurons to glutamate. These results have important implications for understanding the roles of dendritic spines in neuronal integration and plasticity.