Calcium ions are one of the main factors regulating quantal transmitter release and thus synaptic transmission in the nervous system. Using confocal microscopy, fluorescent imaging with the calcium indicator Rhod-2, and time series analysis, we show that the levels of calcium ions inside single synaptic boutons of the lizard neuromuscular junction are not constant at rest, but undergo coordinated fluctuations in the space domain, which cover a large fraction of the synaptic bouton. Furthermore, oscillations in intracellular calcium were frequently observed in the time domain. Control experiments showed no coordinated fluctuations or oscillations at locations outside the synaptic boutons. Edge detection analysis showed that the coordinated fluctuations and oscillations were not due to movement artifacts. No coordinated fluctuations and oscillations were seen when similar measurements and analyses were performed on artificial fluorescent beads. A variance analysis was performed on artificial fluorescent beads and on synaptic boutons. The variance of the fluorescent signal at the synaptic boutons was larger than the variance in artificial beads with the same mean fluorescence. This extra variance was greatly reduced when the extracellular calcium concentration was decreased from 2.0 mM to 0.4 mM. We conclude that the coordinated fluctuations and oscillations in the calcium-induced fluorescence at the synaptic boutons are genuine biological phenomena and may be of significance in the regulation of transmitter release.