Purpose: The purpose of the study was to investigate the electron microscopic findings of the lens epithelial cells (LECs) in patients with Fuchs uveitis syndrome (FUS) who suffered from cataracts and to compare those with age-matched controls. Methods: This study was a prospective, comparative case series. The anterior lens capsules (ALC: basement membrane and associated LECs) were taken from 12 eyes of 12 cases of FUS and ten eyes of ten control patients. The ALCs were obtained from cataract surgery and prepared for transmission electron microscopy (TEM). Results: There were no statistically significant differences regarding the age or gender between the FUS group and the control group (P > 0.05). In the TEM examinations of the ALCs, all of the FUS cases revealed similar significant ultrastructural changes when compared to the control patients. In the FUS group, the LECs showed homogeneous thickening and irregularity which included some small vacuoles in different areas of the epithelial tissue. Moreover, in some areas of the LECs, widespread, oval-shaped, pigment clusters were detected. Conversely, in the control group, the LECs and all of their elements were in normal ultrastructural patterns, with the exception of some small intraepithelial vacuoles which were fewer and smaller than those in the FUS group. Conclusion: Ultrastructural analysis of the ALC of the patients with FUS disclosed some significant alterations which may be related to the summation of oxidative stress, intraocular inflammation, and iris atrophy.