Recent advances of imaging techniques have enabled us to investigate the dynamics of synapses in living neurons. The synapse is constructed of presynaptic and postsynaptic elements which contain various kinds of structural and functional molecules. The postsynaptic density (PSD) is the most prominent structure among the excitatory postsynaptic elements. One of the main components of PSD is the scaffolding proteins which interact with multiple proteins in the synapse. Scaffolding proteins are suggested to play key roles in the emergence, maintenance, and remodeling of the excitatory synapses. Several kinds of scaffolding proteins are known to be present in the mammalian and also other vertebrate brains. These proteins were labeled with green fluorescent protein (GFP) and expressed in cultured neurons to analyze the dynamics and turnover of molecules in the synapses. In this review we describe how these molecules behave when the synapse is newly added or eliminated in the steady state and also when neuronal activity is changed.