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Abstract Background To evaluate the frequency and characteristics of sub-clinical ocular surface squamous neoplasia (OSSN) detected by high-resolution anterior segment tomography (HR- OCT) in patients with clinically unapparent disease following topical treatment. Methods A retrospective chart review of patients with OSSN identified through a pharmacy database at the Bascom Palmer Eye Institute from January 2013 to December 2018 was conducted. Patients undergoing primary therapy with topical 5-fluorouracil 1% (5-FU) (4 times a day for 7 days with a 21-day break) or interferon-alpha-2b (IFN) (4 times a day) were reviewed. Patients were separated into two groups. Group 1 included individuals whose clinical resolution of OSSN aligned with complete resolution on HR-OCT. Group 2 (sub-clinical OSSN group) included individuals with clinical OSSN resolution but with features of persistent disease on HR- OCT. Patients excluded included those treated at an outside institution and those who used topical therapy as a surgical adjunct. Results A total of 95 patients (95 eyes) were reviewed. Sub-clinical OSSN was detected at a frequency of 17% in our study patients (n = 16 patients, 9 treated with 5-FU and 7 treated with IFN). In the 16 individuals, the mean time to clinical resolution was 3.6 ± 1.0 cycles for 5-FU and 4.0 ± 0.0 months for IFN. An additional 2.1 ± 0.8 cycles for 5-FU and 1.2 ± 0.4 months for IFN were needed to achieve HR-OCT resolution of OSSN. Recurrence in Group 1 was noted in 10 patients (12%) while no recurrences occurred in Group 2, the cohort with subclinical disease that received the extended medical therapy. The mean follow-up was 24.0 ± 17.9 months. Conclusion We found that at least 17% of individuals with apparent clinical resolution of OSSN have sub-clinical disease detected on HR-OCT. This information can be used to optimize treatment and extend therapy past the point of clinical resolution.