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The morphology of Drosophila motor terminals changes along the day with a circadian rhythm controlled by the biological clock. Here, we used electron microscopy to investigate the size, number, and distribution of synaptic vesicles, at intervals of 6 h during 2 consecutive days, under light–dark (LD) or the first 2 days in constant darkness (DD). We found changes in the size and distribution of vesicles located either at the active zone or in the reserve pool, indicating a circadian rhythm of synapse reorganization. Vesicles at the active zone were generally smaller than those in the reserve pool in LD and DD conditions. The size of active zones vesicles decreased twice in LD, corresponding with times of more intense locomotion activity, but only once in DD conditions. Synapse 64:14–19, 2010. © 2009 Wiley‐Liss, Inc.