ABSTRACT: BACKGROUND: Bimodal molecular imaging with fluorescence diffuse optical tomography (fDOT) and positron emission tomography (PET) has the capacity to provide multiple molecular information of mouse tumors. The objective of the present study is to co-register fDOT and PET molecular images of tumors in mice automatically. METHODS: The coordinates of bimodal fiducial markers (FM) in regions of detection were automatically detected in planar optical images (x, y positions) in laser pattern optical surface images (z position) and in 3-D PET images. A transformation matrix was calculated from the coordinates of the FM in fDOT and in PET and applied in order to co-register images of mice bearing neuroendocrine tumors. RESULTS: The method yielded accurate non-supervised co-registration of fDOT and PET images. The mean fiducial registration error was smaller than the respective voxel sizes for both modalities, allowing comparison of the distribution of contrast agents from both modalities in mice. Combined imaging depicting tumor metabolism with PET-[18 F]2-deoxy-2-fluoro-D-glucose and blood pool with fDOT demonstrated partial overlap of the two signals. CONCLUSIONS: This automatic method for co-registration of fDOT with PET and other modalities is efficient, simple and rapid, opening up multiplexing capacities for experimental in vivo molecular imaging.