Purpose Through introducing stochastic quantities that can be connected to the dimensions of the microscopic structures exposed to radiations, microdosimetry is concerned with the substantive specifications of radiation quality that could help gain insight into radiation effects. Utilizing the μ-randomness method and Geant4-DNA code, we calculated microdosimetry quantities for nanometric structures in a spherical body of water irradiated with protons. To gain more insight into the effects of radiation on microscopic structures and validate the code parameters, we made a comparison between our results obtained within Geant4-DNA and results from other simulations. Materials and methods We calculated microdosimetric quantities through irradiating a spherical body of water of 6 μm diameter with 0.5–100 MeV protons. Microdosimetric quantities were derived for cylinders with diameter × height values of 23 × 23, 50 × 100, and 300 × 300 Å × Å, which would resemble the typical sizes of sub-cellular organisms such as the DNA, nucleosome, and chromatin fiber. We exploited the concept of μ-randomness to introduce convex bodies of random positions and directions for calculating microdosimetric quantities. We used the Geant4-DNA Monte Carlo simulation toolkit for transporting protons and secondary particles and calculating the frequency- and dose-mean lineal and specific energies in cylindrical volumes. Specifically, for same-sized cylindrical volumes, microdosimetric parameters obtained by Nikjoo et al. using the KURBUC code were used for evaluation. Results For the energy range investigated, the frequency-mean lineal energy, dose-mean lineal energy, frequency-mean specific energy, and dose-mean specific energy vary within [2.34,47.06] (keV/μm), [10.40,68.55] (keV/μm), [0.04,39.38] × 106 cGy, and [0.16,90.29] × 106 cGy, respectively. Regardless of the proton energy, our specific-energy results showed higher sensitivity to volume change, for smaller cylinder volumes rather than larger ones. Regardless of both proton energy and volume of the cylinder under study, we observed a generally better agreement between our frequency-mean, than dose-mean, specific energy results and the KURBUC results. Conclusion Using Geant4-DNA to account for the stochastic nature of energy depositions due to physical interactions between radiation and matter, we calculated microdosimetry parameters concerning proton irradiation. By employing microdosimetry concepts in conjunction with simulation results of our previous work on radiation effects on the DNA, we pinpointed and quantified correlations between microdosimetry parameters and DNA damage. As such, for a volume with comparable mass and mean chord length to the DNA, we could observe the clear correspondence of the mean lineal and specific energy results with the double-strand-break yields of protons in Gy−1.Gbp−1.