Since at least 1552 BC, inflammatory eye disease have been acknowledged as a major threat to sight. There have been a limited number of studies of in vivo inflammatory eye disease in humans and more information is required to improve image interpretation. The aim of this study was to develop and evaluate MRI techniques for the in vivo investigation of retinal damage and macrophage activity in the rat eye affected by experimental autoimmune uveitis (EAU), an inflammatory and autoimmune mediated eye disease. Rat eye structures affected by EAU were visualised in vivo in MR images acquired using figure-of-eight or single loop copper surface coils. Retinal damage in EAU was detected in vivo by MRI at the early stages of EAU. Retinal thickening and detachment in the moderate and severe forms of EAU were monitored in vivo using the same MRI technique. Unlabelled macrophages infiltrating eye structures such as the retina, iris and ciliary body of the rat eye at peak of EAU were visualised in vivo by MRI using a newly-developed single loop, 2-turn surface coil. This study demonstrated that MRI, using specially designed surface coils, can be used for non-invasive in vivo monitoring and also for the in vivo investigation of macrophage activity during development of EAU and of eye disease involving retinal thickening and detachment. The MRI techniques investigated in this study have also demonstrated their potential for the evaluation of new therapies in inflammatory and autoimmune mediated eye disease. All these are non invasive and hence have potential for future possible clinical investigation of inflammatory and autoimmune mediated eye disease or in eye disease involving retinal thickening and detachment.