Stimulation of transient increases in intracellular calcium (Cai2+) activates protein kinases, regulates transcription and influences motility and morphology. Developing neurons generate spontaneous Cai2+ transients, but their role in directing neuronal differentiation and the way in which they encode information are unknown. Here we image Ca2+ in spinal neurons throughout an extended period of early development, and find that two types of spontaneous events, spikes and waves, are expressed at distinct frequencies. Neuronal differentiation is altered when they are eliminated by preventing Ca2+ influx. Reimposing different frequency patterns of Ca2+ elevation demonstrates that natural spike activity is sufficient to promote normal neurotransmitter expression and channel maturation, whereas wave activity is sufficient to regulate neurite extension. Suppression of spontaneous Ca2+ elevations by BAPTA loaded intracellularly indicates that they are also necessary for differentiation. Ca2+ transients appear to encode information in their frequency, like action potentials, although they are 10(4) times longer in duration and less frequent, and implement an intrinsic development programme.