In this work, we investigate ³He magnetic resonance imaging as a non-invasive morphometric tool to assess emphysematous disease state on a local level. Emphysema was induced intratracheally in rats with 25U/100g body weight of porcine pancreatic elastase dissolved in 200 µL saline. Rats were then paired with saline-dosed controls. Nine three-dimensional ³He diffusion-weighted images were acquired at one-, two-, or three-weeks post-dose, after which the lungs were harvested and prepared for histological analysis. Recently introduced indices sensitive to the heterogeneity of the airspace size distribution were calculated. These indices, D₁ and D₂, were derived from the moments of the mean equivalent airway diameters. Averaged over the entire lung, it is shown that the average ³He diffusivity (D_ave) correlates well with histology (R = 0.85, p < 0.0001). By matching small (0.046 cm²) regions in ³He images with corresponding regions in histological slices, D_ave correlates significantly with both D₁ and D₂ (R = 0.88 and R = 0.90, respectively, with p < 0.0001). It is concluded that ³He MRI is a viable non-invasive morphometric tool for localized in vivo emphysema assessment.