A thermodynamic simulation of the phase separation process in a modified thermosetting polymer was carried out. The polydispersity of the generated polymeric species was taken into account in the frame of a conventional Flory-Huggins equation. The example considered in the simulation was a diglycidyl ether of bisphenol-A (DGEBA)-ethylenediamine (EDA), epoxy-amine polymer, modified by the addition of 15 wt% castor oil (monodisperse modifier). The size increase of the oligomeric species and the corresponding decrease of the entropic contribution to the free energy of mixing made a modifier-rich phase (beta-phase) segregate from the matrix (alpha-phase) at a particular conversion level. The beta-phase is enriched in monomers and low-molecular-weight species of the polymer distribution. This produces a significant decrease of the beta-phase conversion with respect to the overall conversion. The monomer with the smaller size and functionality is preferentially segregated into the beta-phase, leading to a stoichiometric imbalance. When a semipermeable beta-phase is assumed, i.e. no oligomeric species are allowed to transfer to the alpha-phase, a secondary phase separation inside the beta-phase is generated. This leads to a sub-matrix (delta-phase) which is rich in modifier, and a sub-segregated phase (gamma-phase) which is rich in thermosetting polymer. This process may continue well beyond the gelation of the alpha-phase, due to the low conversion level of the beta-phase at the time the alpha-phase gels. The thermodynamic simulation explains some recent experimental observations in systems of commercial interest.