Neurons are exquisitely sensitive to the duration, amplitude and localization of transient increases in intracellular Ca²⁺ concentration ([Ca²⁺]_i). Modulation of Ca²⁺ uptake into the mitochondrion and endoplasmic reticulum, and efflux via the plasma membrane Ca²⁺ pump and Na⁺/Ca²⁺ exchange profoundly affect the shape of [Ca²⁺]_i signals. Ca²⁺ clearance mechanisms are modulated by other signaling pathways, are sensitive to metabolic state and have a memory of the recent history of cell activation. We present here examples of pharmacologic and endogenous regulation of Ca²⁺ sequestration and efflux in neurons. Ca²⁺ clearance mechanisms differentially shape [Ca²⁺]_i signals based on their affinity, capacity and location; their modulation alters specific neuronal functions. The increasingly apparent diversity of the molecular entities that make up the [Ca²⁺]_i regulatory system reveals new sites for modulation. Specialized Ca²⁺ clearance mechanisms participate in unique cellular functions and thus, are important targets for pharmacological and physiological regulation of the neuron.