This paper describes a voxel-based method for coregistering microPET [(18)F]FDG emission images and MRI data without the need for fiducial markers. [(18)F]FDG has a well-characterized biodistribution in normal mice and thus may be useful for image registration. Female BALB/c mice were implanted with EMT-6 mouse mammary carcinoma 1 week prior to imaging. Three imaging sessions were performed in which a [(18)F]FDG microPET-R4 emission scan was taken followed by small-animal MRI with and without Gd-based contrast agent. MicroPET and MR images were registered using a voxel-based algorithm that computes rigid-body image transformations based on the alignment of intensity gradients. Registration accuracy was assessed on the basis of dual-modality external fiducial line sources incorporated into the mouse bed. The root mean square (rms) registration errors were 0.74 mm translation and 1.44 degrees rotation without contrast and 0.72 mm translation and 0.89 degrees rotation with contrast. Generally, good registration was evident upon inspection of fused microPET/MR images. Accurate automated, voxel-based microPET-MR image coregistration, utilizing image intensity gradients, is feasible. Our technique requires no manual identification of image features and makes no use of surgically implanted or external fiducial markers or stereotactic apparatus.