The ability to detect molecular probes in deep tissue, based on optical signatures, has been limited by tissue scattering, which reduces the spatial resolution and complicates quantification. To address this challenge, multispectral optoacoustic tomography (MSOT) has been recently introduced, a hybrid technology that capitalizes on the optoacoustic effect to combine rich optical contrast with the high spatial resolution and real-time operation of ultrasound. Using multiwavelength illumination MSOT can visualize molecular probes based on their distinct optical absorption spectra through several millimeters to centimeters of tissue. Herein we present a whole body multi-spectral optoacoustic tomography system and report on spectral processing techniques for detection of molecular probes in living mice.