We developed amniotic membrane ointment (AMO), and the effect of instilling the AMO after photorefractive keratectomy (PRK) was investigated with respect to inflammatory cell infiltration into the corneal stroma, apoptosis of keratocytes, and suppression of lipid peroxidation of cellular walls. The PRK procedure was performed on both eyes of 10 white rabbits. One eye of each rabbit (the experimental eye) was instilled with the AMO and the other eye of the rabbit (the control eye) with a base ointment 0, 8 and 16 h after the PRK procedure. Corneal specimens were collected 24 h after the PRK procedure. Hematoxylin-eosin stain and TUNEL assay were conducted to demonstrate polymorphonuclear and apoptotic cells, respectively. To assess lipid peroxidation, immunohistochemical staining with an antibody to malondialdehyde was undertaken. Compared to the control, the cornea instilled with the AMO had significantly less polymorphonuclear cells infiltrating into the corneal stroma as well as keratocytes subjected to apoptosis. These corneas also showed a significantly less extent of lipid peroxidation than the control. These data support that instillation of the AMO effectively reduced the recruitment of polymorphonuclear cells, the induction of apoptosis in keratocytes, and lipid peroxidation induced by PRK. Thus, this study could provide basic data on the clinical application of the AMO in the days ahead.