Pseudophakic bullous keratopathy (PBK) has become the leading indication for penetrating keratoplasty. In our initial fifty patients having keratoplasty for PBK there was gradual loss of clear grafts in patients with retained intraocular lenses (IOLs). Specular microscopy was performed on donor tissue, and periodically postoperatively, for 130 grafts for PBK. The highest cell loss at one year was in eyes with retained iris support (39.2%) or anterior chamber (37.2%) IOLs. Cell loss in grafts with removed iris support IOLs (21.3%) was significantly less. When iris support IOLs were exchanged for anterior chamber (AC) IOLs, the cell loss at one year (27.1%) was intermediate. We recommend that iris support IOLs be removed at keratoplasty. Exchange for an AC IOL should be considered depending on the visual needs of each patient. Removal of AC IOLs should be based on consideration of prior tolerance and position of the implant.