The concept of nanodosimetry is based on the assumption that initial damage to cells is related to the number of ionizations (the ionization cluster size) directly produced by single particles within, or in the close vicinity of, short segments of DNA. The ionization cluster-size distribution and other nanodosimetric quantities, however, are not directly measurable in biological targets and our current knowledge is mostly based on numerical simulations of particle tracks in water, calculating track structure parameters for nanometric target volumes. The assessment of nanodosimetric quantities derived from particle-track calculations using different Monte Carlo codes plays, therefore, an important role for a more accurate evaluation of the initial damage to cells and, as a consequence, of the biological effectiveness of ionizing radiation. The aim of this work is to assess the differences in the calculated nanodosimetric quantities obtained with Geant4-DNA as compared to those of the ad hoc particle-track Monte Carlo code ‘PTra’ developed at Physikalisch-Technische Bundesanstalt (PTB), Germany. The comparison of the two codes was made for incident electrons of energy in the range between 50 eV and 10 keV, for protons of energy between 300 keV and 10 MeV, and for alpha particles of energy between 1 and 10 MeV as these were the energy ranges available in both codes at the time this investigation was carried out. Good agreement was found for nanodosimetric characteristics of track structure calculated in the high-energy range of each particle type. For lower energies, significant differences were observed, most notably in the estimates of the biological effectiveness. The largest relative differences obtained were over 50%; however, generally the order of magnitude was between 10% and 20%.