The in vivo bioreactor is a hermetically sealed, acellular hydroxyapatite scaffold coated with growth factors that has a pulsating vascular pedicle leash threaded through its center. Tissue-engineered bone is created in weeks while the bioreactor remains embedded under the skin of an animal. The bioreactor also provides a model to study osteogenesis and pathologic scenarios such as tumor progression and metastasis by creating a controlled microenvironment that makes skeletogenesis amenable to genetic and physical manipulation. Animal euthanasia is required to quantitate bioreactor osteogenesis through histomorphometry. Nondestructive measures of new bone growth within the bioreactor are critical to future applications and are the primary questions posed in this study. We compared microcomputed tomography and micro-MRI assessments of bioreactor osteogenesis with conventional histomorphometric measurements in 24 bioreactors and asked if new bone formation could be calculated while the animal was alive. Microcomputed tomography visually, but not numerically, differentiated engineered new bone on its coral scaffold. Dynamic contrast-enhanced micro-MRI demonstrated augmented vascular flow through the bioreactor. Three-dimensional imaging can nondestructively detect tissue-engineered osteogenesis within the implanted bioreactor in vivo, furthering the usefulness of this unique model system.