Increases in cytosolic Ca²⁺ concentration ([Ca²⁺]_i) mediated by NMDA-sensitive glutamate receptors (NMDARs) are important for synaptic plasticity. We studied a wide variety of dendritic spines on rat CA1 pyramidal neurons in acute hippocampal slices. Two-photon uncaging and Ca²⁺ imaging revealed that NMDAR-mediated currents increased with spine-head volume and that even the smallest spines contained a significant number of NMDARs. The fate of Ca²⁺ that entered spine heads through NMDARs was governed by the shape (length and radius) of the spine neck. Larger spines had necks that permitted greater efflux of Ca²⁺ into the dendritic shaft, whereas smaller spines manifested a larger increase in [Ca²⁺]_i within the spine compartment as a result of a smaller Ca²⁺ flux through the neck. Spine-neck geometry is thus an important determinant of spine Ca²⁺ signaling, allowing small spines to be the preferential sites for isolated induction of long-term potentiation.