Although the beneficial effects of perfusion on cell-mediated mineralization have been demonstrated in several studies, the size of the mineralized constructs produced has been limited. The ability to quantify mineralized matrix formation non-invasively within 3D constructs would benefit efforts to optimize bioreactor conditions for scaling-up constructs to clinically relevant dimensions. In this study, we report a micro-CT imaging-based technique to monitor 3D mineralization over time in a perfusion bioreactor and specifically assess mechanisms of construct mineralization by quantifying the number, size, and distribution of mineralized particle formation within constructs varying in thickness from 3 to 9 mm. As expected, mineralized matrix volume and particle number increased with construct thickness. Analyzing multiple concentric volumes inside each construct indicated that a greater proportion of the mineral volume was found within the interior of the perfused constructs. Interestingly, intermediate-sized 6mm thick constructs were found to have the highest core mineral volume fraction and the largest mineralized particles. Two complementary mechanisms of increasing total mineral volume were observed in the 6 and 9 mm constructs: increasing particle size and increasing the number of mineralized particles, respectively. The rate of mineralized matrix formation in the perfused constructs increased from 0.69 mm(3)/week during the first 3 weeks of culture to 1.03 mm(3)/week over the final 2 weeks. In contrast, the rate of mineral deposition in the static controls was 0.01 mm(3)/week during the first 3 weeks of culture and 0.16 mm(3)/week from week 3 to week 5. The ability to monitor overall construct mineralization non-invasively coupled with quantitative analysis of mineralized particle size, number, and distribution offers a powerful tool for elucidating how mineral growth mechanisms are affected by cell type, scaffold material and architecture, or bioreactor flow conditions.