In vitro differentiation of stem cells in biocompatible scaffolds in a bioreactor is a promising method for creating functional engineered tissue replacements suitable for implantation. Basic studies have shown that mechanical, chemical, and pharmaceutical stimuli enhance biological functionality of the replacement as often defined by parameters such as cell viability, gene expression, and protein accumulation. Most of the assays to evaluate these parameters require damage or destruction of the cell-scaffold construct. Therefore, these methods are not suitable for monitoring the development of a functional tissue replacement in a spatial and temporal manner prior to implantation. Bioluminescence imaging is a technique that has been utilized to monitor cell viability and gene expression in various in vivo applications. However, it has never been applied in an in vitro setting for the specific purpose of evaluating a cell-scaffold construct. This research describes the design of flow perfusion bioreactor system suitable for bioluminescence imaging. In the first experimental chapter, the system was tested using MC3T3-E1 cells transfected with a constitutive bioluminescent reporter. It was found that bioluminescence imaging was possible with this system. In the second experimental chapter, MC3T3-E1 cells transfected with BMP-2 linked bioluminescence reporter were cultured by flow perfusion for a period of 11 days. Bioluminescence was detectable from the cells starting at day 4, while peaking in intensity between days 7 and 9. Further, it was also found that bioluminescence occurred in distinct regions within the scaffold. These results indicate that these strategies may yield information not available with current assays. / Master of Science