We present a design for frequency domain instrument that allows for simultaneous gathering of magnetic resonance and diffuse optical tomographic imaging data. This small animal imaging system combines the high anatomical resolution of magnetic resonance imaging (MRI) with the high temporal resolution and physiological information provided by diffuse optical tomography (DOT). The DOT hardware comprises laser diodes and an intensified CCD camera, which are modulated up to 1 GHz by radio frequency (RF) signal generators. An optical imaging head is designed to fit inside the 4 cm inner diameter of a 9.4 T MRI system. Graded index fibers are used to transfer light between the optical hardware and the imaging head within the RF coil. Fiducial markers are integrated into the imaging head to allow the determination of the positions of the source and detector fibers on the MR images and to permit co-registration of MR and optical tomographic images. Detector fibers are arranged compactly and focused through a camera lens onto the photocathode of the intensified CCD camera.