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Most current imaging systems developed for tomographic investigations of intact tissues using diffuse photons suffer from a limited number of sources and detectors. In this paper we describe the construction and evaluation of a large dataset, low noise tomographic system for fluorescence imaging in small animals. The system consists of a parallel plate‐imaging chamber and a lens coupled CCD camera, which enables conventional planar imaging as well as fluorescence tomography. The planar imaging data are used to guide the acquisition of a Fluorescence Molecular Tomography (FMT) dataset containing more than measurements, and to superimpose anatomical features with tomographic results for improved visual representation. Experimental measurements exhibited good agreement with the diffusion theory models used to predict light propagation within the chamber. Tests of the instrument's capacity to …