We are investigating imaging techniques to study the tumor response to photodynamic therapy (PDT). PET can provide physiological and functional information. High-resolution MRI can provide anatomical and morphological changes. Image registration can combine MRI and PET images for improved tumor monitoring. In this study, we acquired high-resolution MRI and microPET [ 18F]fluorodeoxyglucose (FDG) images from C3H mice with RIF-1 tumors that were treated with Pc 4-based PDT. For tumor registration, we developed a finite element model (FEM)-based deformable registration scheme. To assess the registration quality, we performed slice by slice review of both image volumes, computed the volume overlap ratios, and visualized both volumes in color overlay. The mean volume overlap ratios for tumors were 94.7% after registration. Registration of high-resolution MRI and microPET images combines anatomical and functional information of the tumors and provides a useful tool for evaluating photodynamic therapy.