Understanding the three-dimensional distribution of microdamage within trabecular bone may help provide a better understanding of the mechanisms of bone failure. Toward that end, a novel serial milling-based fluorescent imaging system was developed for quantifying microscopic damage in three dimensions throughout cores of trabecular bone. The overall goal for this study was to compare two-dimensional (2D), surface-based measures of microdamage extracted from this new imaging system against those from more conventional histological section analyses. Human vertebral trabecular cores were isolated, stained en bloc with a series of chelating fluorochromes, monotonically loaded, and underwent microdamage quantification via the two methods. Bone area fraction measured by the new system was significantly correlated to that measured by histological point counting (p < 0.001, R² = 0.80). Additionally, the new system produced statistically equivalent (p = 0.021) measures of damage fraction (mean ± SD), Dx.AF = 0.047 ± 0.021, to that obtained from stereological point counting, Dx.AF = 0.048 ± 0.017, at a 10% difference level. These results demonstrate that this serial milling-based fluorescent imaging system provides a destructive yet practical alternative to more conventional histologic section analysis in addition to its ability to provide a better understanding of the three-dimensional nature of microdamage.