Objective: To perform full-length sequencing of extrachromosomal circular DNA (eccDNA) in the lens capsule of patients with human immunodeficiency virus (HIV)-infected complicated cataract (CC) and age-related cataract (ARC). The aim is to analyze the molecular characteristics and potential functions of eccDNA and initially investigate the mechanism by which eccDNA contributes to the pathogenesis of cataract related to HIV infection. Methods: Lens capsules were collected from 4 CC patients who were co-infected with HIV and from ARC patients matched for gender and age. The eccDNA was sequenced following a process that included extraction, rolling circle amplification, and circle-seq. We then analyzed and compared the number, length distribution, genomic element distribution, and enrichment of differential gene functions associated with eccDNA in the lens capsules of CC patients co-infected with HIV and ARC patients. Results: The number of eccDNA molecules in the lens capsule of CC patients co-infected with HIV was significantly higher than that in ARC patients, while the GC content was lower.. In both CC and ARC patients, the majority of eccDNA lengths felll within the range of 1200 to 1800 bp. However, CC patients exhibited an additional peak between 2000 and 2200 bp, where the abundance of eccDNA in the ARC group was extremely low. Regarding genomic elements derived from eccDNA, the proportion in CC patients was lower than that in the ARC group within CpG islands. The pathways associated with differential gene enrichment of eccDNA in CC patients were primarily related to the calcium signaling pathway, Apelin signaling pathway, and cGMP-PKG signaling pathway. Conclusions: There are notable differences in the molecular characteristics of lens capsule eccDNA between CC patients with HIV infection and ARC patients.These finding suggest that eccDNA may influence the onset and progression of CC by regulating the metabolic functions of the anterior lens capsule through gene expression.