Acute anterior uveitis (AAU) and related spondyloarthropathies (SpAs) such as ankylosing spondylitis, reactive arthritis and psoriatic arthritis have joined the expanding family of inflammatory disease associated with the biology of the intestinal microbiome. This review discusses why AAU and related SpAs have been incorporated into this paradigm shift for understanding disease pathogenesis. We focus in particular on the major risk gene HLA-B27 and how it may be associated with the loss of intestinal tolerance and ocular immune privilege that may accompany AAU. We discuss how perturbed microbiota composition, intestinal immunity and/or barrier function may contribute to the development of inflammatory responses that ultimately target either self or microbial antigen in the eye. These inflammatory processes may be augmented by translocation of intestinally-derived innate immune stimuli, such as microbe associated molecular patterns (MAMPs). Moreover, gut-derived host immune cells or damage-associated molecular patterns (DAMPs) may contribute to the ocular inflammatory cascade. Finally we discuss the novel therapeutic avenues offered by the microbiota for future clinical management of AAU and spondyloarthropathies.