Structure and behavior of amphiphilogel nanoparticles as a drug carriers for cyclosporine A (CsA) have been studied by the molecular modeling using empirical force field. Five atomistic models of a gel-based emulsions (GEM) with various gel compositions have been investigated in order to find a system most similar to a sixth atomistic model of self-microemulsifying drug delivery system (SMEDDS) taken as an exemplar of CsA delivery system. Structural parameters and energy characteristics (i.e. non-bond interaction energy between CsA and whole remaining components of a gel nanoparticle, CsA/gel nanoparticle intermolecular non-bond interaction energy, CsA–gel molecule pair interaction energy, volume fraction, concentration profiles and number of pervaded water molecules) of these six models in a waterless form and in a water containing form have been studied in dependence on the composition. The Flory–Huggins theory as implemented in the Accelrys Materials Studio 4.2 modeling environment was used to study the pair interactions of cyclosporine A with various types of surfactants. Structural parameters and energy characteristics of all systems have been compared and one composition was selected as a very promising for further experimental study.