To evaluate and compare endothelial features by in-vivo confocal microscopy (IVCM) in Chinese eyes with chronic or recurrent anterior uveitis (AU) with and without cytomegalovirus (CMV). A double-masked, cross-sectional case-control study at a tertiary eye clinic. Thirty eyes of 30 subjects were analyzed. Fifteen eyes (50%) were CMV positive, while fifteen eyes were negative for herpes simplex virus, varicella zoster virus and CMV. Absence of pseudoguttata was the strongest, independent risk factor for CMV (OR 34.53, 95% CI: 1.84-648.02, p = 0.018), followed by severe iris depigmentation (OR 31.45, 1.02-965.81, p = 0.048) and low corneal endothelial cell density (ECD) (OR 14.79, 1.14-191.30, p = 0.039) on univariable regression. All three remained statistically significant after adjustment. The combination of absence of pseudoguttata and low ECD on IVCM achieved a similar predictive value as iris depigmentation examination. Absence of pseudoguttata on IVCM was an independent predictor of positive CMV detection after adjusting for iris depigmentation and corneal endothelial cell density. The addition of this feature to severe iris depigmentation and low corneal ECD can increase the positive predictive value of detecting CMV. IVCM was a useful non-invasive tool to predict CMV in patients with chronic or recurrent AU.