In this research the influence of aeration mode and time of the storage on selected features of aerated agar based confectionery filling with vanilla flavouring was determined. Samples obtained by introducing compressed air had significantly lower density and higher porosity, and the time of storage did not have a significant influence on the density and porosity of the filling. Both the aerated agar filling and the chocolate coating of the vanilla flavoured aerated agar based confectionery filling created heterogenic and multiphase structures, wherein during the time of the storage the water activity present, caused by diffusion and secretion of the water, were a result of the syneresis of the agar gel and the crystallization of its components. These processes caused significant changes in the rheological parameters of the filling, showing changes in its structure. The obtained rheological parameters (the work of the compression and relaxation moduli) confirmed higher elasticity of the samples obtained by mode A and showed that the aeration level caused faster damage to the structure of the samples.