A study of caffeine effects on the complexation of the DNA molecule with Cu²⁺ and Mg²⁺ ions in solution is presented. DNA binding with cations and caffeine is traced from changes in DNA circular dichroism and UV absorption spectra. The complexation of caffeine with M²⁺ ions is studied by IR spectroscopy. Caffeine is found to form complexes of different structure with Mg²⁺ and Cu²⁺ ions in solution. In the presence of caffeine, DNA solutions with MCl₂ show signs of formation of intricate complexes involving nitrogenous bases. In DNA solutions with CuCl₂, the presence of caffeine causes additional destabilization of the secondary DNA structure. In DNA solutions with MgCl₂, the presence of caffeine leads to the formation of new complexes with the participation of Mg²⁺, caffeine, and bases without disrupting the secondary DNA structure.