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Two cases of necrotizing keratitis following laser refractive corneal surgery, with stable and controlled Crohn’s disease are described. A 40-year-old woman developed bilateral stromal inflammation and inferior thinning in the right eye along the flap edge within 1 day of uneventful bilateral IntraLase laser-assisted in situ keratomileusis. The other case is a 30-year-old man who also developed bilateral inferior stromal infiltrates 2 days following photorefractive keratectomy. Both cases were aggressively treated with systemic and topical corticosteroids. The infiltrates in both patients gradually resolved, with one relapse during the 7 months period of follow-up in the first case. These cases highlight the importance of taking precautions considering this and similar autoimmune conditions as a relative contraindication to refractive surgery.