The design of efficient cationic lipid and peptide nanocarriers for oligodeoxynucleotide (ODN) delivery into cells requires precise understanding and control of their physical properties. In this work we used X-ray diffraction, fluorescence resonance energy transfer (FRET), dynamic light scattering (DLS) and zeta-potential measurements to characterize the stability of the nanoparticles formed by ODN with cationic phospholipids and with a native cationic peptide, protamine. The most important findings can be summarized as follows: 1) ODNs form stable complexes with protamine and cationic phospholipids at salt concentrations below ~0.5 and ~0.3 M NaCl, respectively. 2) The ODN lipoplexes are typified by tightly packed lamellar phases and disordered ODN arrangement between the lipid bilayers. 3) ODN/protamine complexes with positive zeta-potentials gradually increase in size in the course of hours and days, while the size of nanoparticles with negative zeta-potentials remains constant. 4) There are significant differences between ODN/lipid and ODN/protamine particle size distributions. The former displayed a characteristic maximum at cationic/anionic 1:1 charge ratio, while the latter were not influenced by variations of the ODN/protamine ratio.