Uveitis is a major cause of visual impairment. Most uveitis cases have autoimmune etiology. Pediatric autoimmune uveitis may be associated with systemic diseases such as juvenile idiopathic arthritis or may arise as an isolated disorder. It may be accompanied by retinal vasculitis due to retinal microcirculation involvement. Nailfold capillaroscopy, a digital microscope, is a non-invasive tool for systemic microcirculation evaluation. We aimed to evaluate systemic microcirculation abnormalities in pediatric autoimmune uveitis. Twenty-five patients with pediatric autoimmune uveitis and 21 healthy children underwent detailed capillaroscopic evaluation. We assessed capillary density/mm, capillary morphology, capillary dimensions, and the presence or absence of microhemorrhages and avascular areas. The mean age of the study and control groups was 11.24 ± 3.03 and 9.9 ± 4.17years, respectively. Most included patients had isolated uveitis and juvenile idiopathic arthritis (64% and 24%, respectively). The predominant uveitis subtype in the study was anterior uveitis (48%). A significant difference was found between cases and controls regarding mean capillary density (p-value = 0.0003) and the number of subjects having capillary density less than 7 (p-value = 0.002). Other capillaroscopic abnormalities did not show any significant difference between the studied groups. Mean capillary density did not correlate significantly with age, disease duration, or acute phase reactants. Children with autoimmune uveitis, whether isolated or asa part of systemic disease, may have systemic microcirculation involvement. Key Points • Idiopathic autoimmune uveitis is not always an isolated intraocular condition. • Systemic microcirculation involvement may occur in pediatric autoimmune uveitis, even in cases with isolated uveitis. • Nailfold capillaroscopy showed that capillary density in children with autoimmune uveitis is significantly reduced compared to healthy controls.