Hybrid NIR-MRI imaging has been used in a clinical breast imaging system to characterize breast tissue properties. The multi-spectral, frequency-domain tomography system operates inside a clinical scanner via long silica-glass optical fiber bundles and using a non-magnetic fiber-patient interface attached to a high resolution MR breast coil. Sixteen fiber bundles are positioned around the circumference of the female breast yielding 240 measurements of light transmission (amplitude and phase) at six optical wavelengths from 660-850nm through up to 12 cm of tissue. From optical measurements, we use a Newton-type algorithm to reconstruct images of tissue optical properties (absorption and scattering), and physiological tissue features such as oxy-hemoglobin [Hb-O2], deoxy-hemoglobin concentrations [Hb-R], water concentration [water], scattering amplitude, and scattering power. We are exploring the synergistic benefits of a combined NIR-MRI data set, specifically the ways in which MRI (i.e. high spatial resolution) can be used to enhance NIR (i.e. high contrast resolution) image reconstruction. A priori knowledge can be applied to image reconstruction in the form of spatial and spectral constraints to improve spatial resolution, contrast, and quantitative accuracy of NIR images. In vivo results suggest that this combined system can accurately quantify contrast between the properties of tissues present in the breast (i.e. adipose and fibroglandular) regardless of their varied and complex spatial organization. For a group of healthy female volunteers, we observe greater contrast between the properties of adipose and glandular tissues when we use MR-guidance than when we do not, and values of total hemoglobin and water content are more consistent with what is physiologically expected.