As we move into the new millennium, it is important that we improve our understanding of radiation effects on humans and nanoelectronic systems. This understanding is essential in a number of areas including radiation therapy for cancer treatment and extended human presence in outer space. Nanodosimetry in low-pressure gases enables measurement of the energy deposition of ionizing radiation on a scale equivalent to the dimensions of the DNA molecule. This is extremely important for not only biological applications but also electronic applications, as the effect of radiation on nanoelectronics needs to be determined before they are installed and deployed in complex radiation fields. However, before nanodosimetry can be widely applied, further investigation is required to link the output of gas-based nanodosimeters to the actual effect of the radiation on a biological or electronic system. The purpose of this research is to conduct nanodosimetric measurements of proton radiation fields at the proton accelerator of Loma Linda University Medical Center (LLUMC) and to develop a Monte Carlo simulation system to validate and support further developments of experimental nanodosimetry. To achieve this, measured ion cluster size distributions are compared to the output from the Monte Carlo simulation system that simulates the characteristics of the LLUMC beam line and the performance of the nanodosimeter installed on one of LLUMC's proton research beam lines. © 2004 IEEE.