We describe longitudinal measurements of functional residual capacity (FRC) in breathing mice using a clinical computed tomography (CT) scanner. Lungs of anesthetized mice from the A/J and C3H/HeJ strains were scanned over a 10-s period. Using a fixed threshold for CT density, we could accurately and reproducibly obtain the amount of air in the lungs at FRC, with a 10% coefficient of variation. Total lung volume, and the fractions in left and right lungs, were measured in the two strains from 4 to 12 wk of age. Results show that in both strains the FRC increases only up to 6 wk of age and then remains stable despite a steady increase in body weight. Over this time period, FRC was consistently about 50% greater in the C3H/HeJ strain compared with the A/J strain. The C3H/HeJ strain also has a significantly smaller fraction of the total lung volume in the left lung. We conclude that accurate measurements of FRC in breathing mice can be made using a standard clinical CT scanner. This method may be useful for repeated noninvasive assessment of both structural and functional changes in the lungs of experimental and genetically manipulated mice.