High-energy, high-charge (HZE) radiation, including iron ions ((56)Fe(26+)), is a component of the space environment. We recently observed a profound loss of trabecular bone in mice after whole-body HZE irradiation. The goal of this study was to examine morphology in bones that were excluded from a (56)Fe(26+) beam used to irradiate the body. Using 10-week-old male Sprague-Dawley rats and excluding the hind limbs and pelvis, we irradiated animals with 0, 1, 2 and 4 Gy (56)Fe(26+) ions and killed them humanely after 9 months. Animals grew throughout the experiment. Trabecular bone volume, connectivity and thickness within the proximal tibiae were significantly lower than control in a dose-dependent manner. Irradiated animals generally had less body mass than controls, which largely accounted for the variability in bone parameters as determined by ANCOVA. Likewise, lower cortical parameters were associated with reduced mass. However, lesser trabecular thickness in the 4-Gy group could not be attributed to body mass alone. Indicators of bone metabolism were generally unchanged, suggesting stabilized turnover. Exposure to (56)Fe(26+) ions can alter trabecular microarchitecture in shielded bones. Reduced body mass seems to be correlated with these deficits of trabecular and cortical bone.