To present two cases of delayed-onset postoperative endophthalmitis following trabeculectomy combined with mitomycin C for secondary glaucoma after penetrating keratoplasty. We retrospectively evaluated two patients with late endophthalmitis after trabeculectomy combined with intraoperative mitomycin C application. Both patients underwent trabeculectomy for uncontrolled glaucoma following penetrating keratoplasty and they developed thin-walled cystic blebs. Intraocular pressure was normal, and grafts remained clear postoperatively. Severe endophthalmitis with hypopyon developed at 3 and 7 months postoperatively. Both patients had concomitant bleb infection. They underwent vitreous sampling and intravitreal injection of vancomycin and amikacin and were given topical fortified and systemic antibiotic therapy. Intravitreal injection was repeated once in both patients. Cultures grew Streptococcus pneumonias in one and Staphylococcus aureus in the other. Although the treatment of endophthalmitis was successful in both patients, only one of them achieved useful vision (20/40). For the other patient who had been infected with S. pneumoniae, vision was light perception. Delayed-onset endophthalmitis following trabeculectomy with mitomycin C application is a severe and vision threatening complication. It seems that the development of thin cystic filtering blebs secondary to intraoperative mitomycin C application may be a predisposing factor for bleb-related late endophthalmitis.