To identify the risk of relapse and subclinical inflammatory stages of systemic autoimmune diseases, new tools are needed. In the recent years, choroidal thickness and retinal thickness measured with ocular coherence tomography (OCT) have been proposed as an inflammatory marker for different systemic diseases, especially for conditions with a vascular component. Our aim in this article is to review the literature regarding the role of choroidal and retinal thickness as a potential inflammatory marker in systemic autoimmune and inflammatory diseases measured by OCT. Current literature suggests that the choroid of patients thickens in active phases of inflammatory diseases with vascular involvement. This pattern is observed in lupus, systemic sclerosis, Behçet disease, spondylitis, and familial Mediterranean fever. Choroidal thickness may decrease with biological treatments, along with systemic inflammation. Repeated flares and long-term disease, however, may thin the choroid, as a result of prolonged insult to the microvasculature and subsequent atrophy. Less is known about the effect of these diseases on retinal thickness. In summary, choroidal and retinal thickness measured by OCT may be promising markers for inflammation in systemic autoimmune and inflammatory diseases; however, more studies are warranted before generalizing choroidal thickness measurements by OCT as a marker for disease activity. The role of retinal thickness is more unclear due to a lack of studies in this field.