Hydroxyapatite (HAp) was modified by the action of various hydrophobic agents based on silicon-containing compounds. The influence of the type of applied agent on the thermodynamic and kinetic parameters of the cross-linking of poly(dimethyl siloxane)/HAp composites was investigated. All the modified HAp particles became hydrophobic and these samples were used to synthesize the polysiloxane/hydroxyapatite composites (PDMS/HAp). The possible modes of interaction between the hydroxyapatite and hydrophobing agents were discussed. The most probable interaction between hydroxyapatite and the applied hydrophobing agents is hydrogen bonding. PDMS/HAp composites were formed directly in the cell of the DSC and cross-linking was investigated in situ. It was determined that the introduction of hydroxyapatite into polysiloxane matrices changed the enthalpy of cross-linking, as well as the activation energy of cross-linking and reaction order, while the introduction of modified HAp led to thermodynamic and kinetic parameters more similar to those of the cross-linking of unfilled elastomer.