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For imaging problems in which numerical solutions need to be computed for both the inverse and the underlying forward problems, discretization can be a major factor that determines the accuracy of imaging. In this work, we analyze the effect of discretization on the accuracy of fluorescence diffuse optical tomography. We model the forward problem by a pair of diffusion equations at the excitation and emission wavelengths and consider a finite element discretization method for the numerical solution of the forward problem. For the inverse problem, we use an optimization framework which allows incorporation of a priori information in the form of zeroth- and first-order Tikhonov regularization terms. Next, we convert the inverse problem into a variational problem and use Galerkin projection to discretize the inverse problem. Following the discretization, we analyze the error in reconstructed images due to the discretization of the forward and inverse problems and present two theorems which point out the factors that may lead to high error such as the mutual dependence of the forward and inverse problems, the number of sources and detectors, their configuration and their positions with respect to fluorophore concentration, and the formulation of the inverse problem. Finally, we demonstrate the results and implications of our error analysis by numerical experiments. In the second part of the paper, we apply our results to design novel adaptive discretization algorithms.