MultiSpectral Optoacoustic Tomography (MSOT) is an emerging modality that combines the high contrast of optical imaging with the spatial resolution and penetration depth of ultrasound, to provide detailed images of hemoglobin concentration and oxygenation. To facilitate accurate determination of changes in the vascularity and oxygenation of a biological tissue over time, for example, a tumor in response to cancer therapy, an extensive study of stability and reproducibility of a small animal MSOT system has been performed. Investigations were first made with a stable phantom imaged repeatedly over time scales of hours, days and months, to evaluate the reproducibility of the system over time. We found that the small animal MSOT system exhibited excellent reproducibility with a coefficient of variation (COV) in the measured MSOT signals of less than 8% over the course of 30 days and within 1.5% over a single day. Experiments performed in vivo demonstrated the potential for measurement of oxyhemoglobin over time in a realistic experimental setting. The effect of breathing medical air or oxygen under conditions of fixed respiration rate and body temperature within normal organs, including the spleen and kidneys, were investigated. The COV for oxyhemoglobin signals retrieved from spectral unmixing was assessed within both biological (different mouse) and imaging (different scan) replicates. As expected, biological replicates produced a large COV (up to 40% within the spleen) compared to imaging replicates within a single mouse (up to 10% within the spleen). Furthermore, no significant difference was found between data acquired by different operators. The data presented here suggest that MSOT is highly reproducible for both phantom and in vivo imaging, hence could reliably detect changes in oxygenation occurring in living subjects.