This article summarizes the basic principles of confocal microscopy and how they can be employed to visualize synaptic structure and function. Optical 'sectioning' of living cells allows the examination of a large number of biological processes at different subcellular localities. Different fluorescent markers enable the study of processes in the extracellular, intracellular and membrane domains of the nerve cell. The excellent spatial resolution of confocal microscopy permits to study the changes in intracellular calcium concentration in single synaptic boutons, without a substantial interference from supporting cells. Intracellular calcium concentration shows coordinated fluctuations in space and periodic oscillations. Periodic oscillations can serve as time keeping devices in nerve terminals. Oscillations were previously observed also in the process of transmitter release. We speculate therefore that these calcium oscillations may be of significance, if the quantal transmitter release is governed by a sequence of calcium dependent steps, which have a different affinity for calcium.