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Objective: To compare the conjunctival morphological changes in patients with Hashimoto�s thyroiditis (HT) without thyroid-associated ophthalmopathy (TAO) and controls using impression cytology technique. Material and Method: We included 25 HT patients and 33 healthy controls who did not have TAO findings or dry eye. For both groups, thyroid stimulating hormone (TSH), free T4(FT4), and anti-thyroid peroxidase (anti-TPO) were measured. Thyroid ultrasonography was performed, together with all routine eye check-ups and the Schirmer's test. Also, conjunctival impression cytology (CIC) test was performed to analyze the conjunctival morphology. Results: When the CIC of HT patients was observed; 12% had grade 0, 40% had grade 1, 28% had grade 2 and 20% had grade 3. While patients with squamous metaplasia made up 48% of the HT group, this was observed at 6.1% in the control group (p < 0,001). In the regression model formulated, it was observed that obesity (OR=7.500; p=0.017) and anti TPO levels (OR=1.370, p=0,007) were independent stipulations for the squamous metaplasia. Conclusion: Conjunctival squamous metaplasia was more frequently seen in HT than controls and serum Anti-TPO level and obesity were detected as independent predictors of the worsening at the conjunctival impression cytology.