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Objective: To evaluate the efficacy and risks of complications of pulse dosing of topical 5-fluorouracil (5-FU) in the treatment of corneal intraepithelial neoplasia (CIN), and conjunctival squamous cell carcinoma (SCC)., Design: Prospective, noncomparative case series., Participants: Fifteen patients with histological evidence CIN or SCC of the conjunctiva and cornea were identified by tumor biopsy., Methods: All patients clinically evident of CIN, or SCC were evaluated, with maximum 30 months of follow-up were treated with pulsed dosing of 1% 5-FU. Treatment cycles were defined as four times per day for 4 days using the medication followed by 30 days without medication. The number of initial treatment was six cycles., Results: The mean age of the 15 patients was 50.8 years (range 25-78 years). Excision biopsy proved seven cases as CIN, and eight cases as locally invasive SCC. All patients remained disease free with a mean follow-up of 14.53 months (range 6-30 months). Additional chemotherapy was given after the initial treatment cycles, only for one case. 5-FU caused mild temporary local irritation, but no long-term intraocular or extra ocular complications., Conclusions: Adjuvant 1% topical 5-FU appears to be effective in the prevention of recurrence of conjunctival or corneal CIN and SCC after excision biopsy. Our results indicate that at least six cycles of topical 1% 5-FU is required to prevent local recurrence in the long term. It is well-tolerated and an effective method of treatment. No complications that would preclude use of our dose regimen were noted.