Protein liquid phase transition into a solid state has been proposed as a mechanism for the onset of pathological protein aggregate formation in neurodegenerative diseases, such as Alzheimer’s and Parkinson’s diseases. The synaptic vesicle (SV) cluster is one of the compartments that is proposed to be organized by liquid-liquid phase separation (LLPS), in which the phosphoprotein synapsin plays the key role. To determine possible involvement of the synaptic vesicle liquid phase in pathological transformations it is important to know how this phase is functionally regulated. In addition to synapsin, SV clusters contain an array of proteins with SH3 domains, some of which interact with synapsin. It the current study we investigated the localisation and regulation of the SH3 domain-containing protein endophilin A in the organization of the synaptic vesicle liquid phase in identified inhibitory and excitatory synapses.