The lens capsule and silicone intraocular lens (IOL) extracted from the eye of a patient with chronic infectious endophthalmitis was examined histopathologically to evaluate the pathology of a capsule and IOL surfaces in the presence of bacterial infection. A 69-year-old man developed an infection in his right eye 4 months after phacoemulsification and aspiration of a cataract and implantation of a silicone IOL. During vitrectomy, the capsule and IOL were extracted and processed for light or scanning electron microscopy. Cryosections of the capsule were subjected to Gram staining and immunohistochemical tests for extracellular matrix components. The lens capsule contained an accumulation of extracellular matrix, including collagen types and fibronectin. A colony of Gram-positive rod bacteria was detected inside the capsular bag. Scanning electron microscopy failed to detect any microorganisms on the IOL surface. Histological examination of cryosections of the extracted capsule confirmed the presence of infection during surgery even though preoperative cultures of intraocular fluid were negative. Immediate antibacterial treatment could be initiated.