To clinically and molecularly characterize a group of patients with progressive limbal stem cell deficiency (LSCD) due to aniridic keratopathy (AK), but with minimally affected irides. Retrospective case series. A total of 12 eyes of 6 patients who underwent keratolimbal allograft (KLAL) for AK in the absence of the classic stigmata of aniridia at the Cincinnati Eye Institute/University of Cincinnati between 2000 and 2007. Retrospective chart review. Ocular surface stability after KLAL and change in visual acuity. Subjects' mean age was 32.57 years, 66% were female, and mean follow-up was 64.4 months (range, 20-115 months). All patients presented with a decline in their vision secondary to LSCD. Average preoperative best-corrected visual acuity (BCVA) logarithm of the minimum angle of resolution (logMAR) was 1.4 (range, 0.10-2.8). All patients had minimally affected irides with subtle abnormal findings, including ectropion uveae and stromal atrophy. All patients developed severe LSCD and required KLAL. Average postoperative logMAR BCVA was 0.35 (range, 0.00-1.00). All ocular surfaces remained stable throughout the follow-up period. Family history consistent with autosomal dominant inheritance was positive in 4 of 6 patients. PAX6 genetic testing identified 2 pathologic mutations and 1 possible disease-causing variant. Aniridic keratopathy may present in the absence of other classic stigmata of aniridia and be associated with minimally affected irides. A subset of these patients has definitive mutations in PAX6 and once identified can be counseled appropriately. These patients respond well to KLAL and may therefore benefit from early detection.