Excitation emission spectroscopy (EES) has been used in the past to characterize many different types of tissue. This technique uses multiple excitation wavelengths and samples a complete optical spectrum for each, yielding an excitation-emission matrix (EEM). Upon study of the EEM, it is possible to determine the presence of multiple optical contrast agents since these dyes can have characteristic spectra that can be separated. Here, we demonstrate EES specifically designed for use in conjunction with MR. This EES is applied with an in-suite control setup that permits real-time navigation, utilizing active MR tracking catheters, and providing a platform for MR-guided tissue characterization. The EES system is used in a demonstration experiment to highlight MR imaging, MR guidance in conjunction with a catheter-based optical measurement.