In this study, the upper-limit volume (gas plus partial tissue volume) as well as absolute volume (gas only) of lungs measured with hyperpolarized (3)He-MR imaging is compared with that determined by micro-computed tomography (CT) under similar ventilation conditions in normal rats. Five Brown Norway rats (210-259 g) were ventilated with O(2), alternately with (3)He, using a computer-controlled ventilator, and 3D density-weighted images of the lungs were acquired during a breath hold after six wash-in breaths of (3)He. The rats were then transferred to a micro-CT scanner, and a similar experimental setup was used to obtain images of the lungs during a breath hold of air with an airway pressure equal to that of the MR imaging breath hold. The upper-limit and absolute volumes obtained from (3)He-MR and micro-CT methods were not significantly different (p > 0.05). The good agreement between the lung volumes measured with the two imaging methods suggests that (3)He-MR imaging can be used for quantitative analysis of lung volume changes in longitudinal studies without the exposure to the ionizing radiation which accompanies micro-CT imaging.