Herein we demonstrate the construction of the first reported fluorescence animal tomographer for molecular investigations of cancer-associated expression patterns. Using inversion techniques that account for the diffuse nature of photon propagation in tissue and near infrared fluorescent molecular beacons we were able to obtain three-dimensional in-vivo images of cathepsin B expression of orthopic gliomas. We demonstrate that fluorescent probes, activated by carcinogenesis, can be detected with high positional accuracy and high sensitivity in deep tissues, that molecular specificities of different beacons towards enzymes can be resolved, and that tomography of beacon activation is linearly related to enzyme concentration. The tomographic imaging method offers a range of new capabilities for studying biological function using fluorescent chemical sensors, for identifying molecular expression patterns via multispectral imaging and for continuously monitoring drug therapies. It is envisaged that molecular sensing will significantly improve the detection capacity of early cancer since malignancy identification is based on the molecular signals responsible for carcinogenesis and not on structural or functional tissue changes inflicted by well-formed cancers that are currently targeted by traditional medical imaging techniques.