Experimental autoimmune uveoretinitis (EAU) in mice is a model for human autoimmune uveitis. Longitudinal follow-up is only possible by non-invasive techniques, but the information obtained by visual fundus examination can be limited. We therefore evaluated the efficacy of optical coherence tomography (OCT) and electroretinography (ERG) to monitor pathological and functional changes of the retina in vivo. OCT imaging and ERG recording as a measure of visual function were compared with visual fundoscopic imaging and histology findings in the same mouse. Our results showed that OCT imaging of the retina was well correlated with clinical and histological observations in mice during EAU. However, OCT imaging was more sensitive than fundoscopic imaging in detecting the cell infiltrates at the early phase of disease onset. Furthermore, by allowing multi-layer cross- and horizontal-sectional visualizations of retinal lesions longitudinally in a noninvasive fashion, OCT added information that could not be obtained by fundoscopic and histological examinations. Lastly, retinal thickness obtained by OCT imaging provided a key indicator reflecting disease activity, which showed a close association with visual dysfunction as measured by ERG recordings in EAU mice. Thus, our findings demonstrate that OCT is a highly sensitive and reliable technique, and a valuable method for the semi-quantitative evaluation of retinal inflammation in vivo in the mouse.