Energetics of chitosan (CS) polyplexes and conformational stability of bound DNA were studied at pH 5.0 by ITC and HS–DSC, respectively. The CS–DNA binding isotherm was well approximated by the McGhee–von Hippel model suggesting the binding mechanism to be a cooperative attachment of interacting CS ligands to the DNA matrix. Melting thermograms of polyplexes revealed the transformation of different conformational forms of bound DNA in dependence on the CS/DNA weight ratio rw. At 0<rw<0.7 two conformational forms were observed and assigned, respectively, to the intact (free) and globular (bound) DNA. A contribution of the globular DNA to the melting enthalpy approached 100 % at the equivalent weight CS content. At higher CS contents a further stabilization of the globular DNA conformation was detected and assigned to the DNA globules in overcharged polyplexes. The polyplex dissociation was studied at pH 7.4 under conditions of zero and a physiological concentration of NaCl. Phase separation of the system was observed in both cases. DNA was almost completely immobilized in the lower phase enriched with CS. At physiological ionic strength, DNA converted from the globular to the intact form although remained to be immobilized in the CS phase.