BACKGROUND To report two cases of corneal infection after Descemet stripping automated endothelial keratoplasty (DSAEK). METHODS Two eyes of two patients demonstrated varying clinical presentations of microbial keratitis after DSAEK. At the initial presentation, the keratitis involved the host cornea alone in case 1, whereas in case 2, the posterior lamellar disk alone was involved. A pair of microvitrectomy scissors was used in case 2 from the side port to obtain a 2-mm sample of the posterior lamellar disk for microbiologic evaluation. The keratitis did not respond to medical therapy, and therapeutic penetrating keratoplasty was performed to resolve the infection in both the eyes. The main outcome measures were resolution of infection, absence of recurrence of keratitis, graft clarity, and visual outcome. RESULTS There was complete resolution of infection after full thickness therapeutic grafts with best-corrected visual acuities of 20/60 and 20/40, respectively. CONCLUSIONS Initial presentation of microbial keratitis after DSAEK may involve either the host or the posterior lamellar disk alone. A microvitrectomy scissors through the side port may be used for biopsy of posterior lamellar disk in recalcitrant infection.