A major difficulty arising from whole-body optoacoustic imaging is the long acquisition times associated with recording signals from multiple spatial projections. The acquired signals are also generally weak and the signal-to-noise-ratio is low, problems often solved by signal averaging, which complicates acquisition and increases acquisition times to an extent that makes many in vivo applications challenging or even impossible. Herein we present a fast acquisition multispectral optoacoustic tomography (MSOT) scanner for whole-body visualization of molecular markers in small animals. Multi-wavelength illumination offers the possibility to resolve exogenously administered fluorescent probes, biomarkers, and other intrinsic and exogenous chromophores. The system performance is determined in phantom experiments involving molecular probes and validated by imaging of small animals of various scales.