The monitoring of the progress of mineralization is traditionally performed by biochemical or molecular methods.  Using 3-dimensional (3-D) cell systems may lead to difficulties in using normal methods. This project aims to develop analytical methods for monitoring in vitro extracellular matrix mineralization on scaffolds using x-ray µCT technology, 3-D modeling processes and computational methods. µCT scanned scaffolds seeded with or without mouse pre-osteoblasts. Upon completion scaffolds were fixed in 4% paraformaldehyde and re-scanned using µCT and the data imported into the MIMICS software, and analyzed for gray value mean density and gray value gradient distribution in a defined layer including the scaffold surface.  According to preliminary results, the mean gray value in the investigated layer changes on going from an empty scaffold to 3, 6 and 8 weeks differentiated scaffolds. SEM observations support the µCT data. It is possible to detect and quantify extracellular matrix mineralization on 3-D surfaces using x-ray µCT data and advanced 3-D computational methods.