To compare the conjunctival morphological changes in patients with Hashimoto’s thyroiditis (HT) without thyroid-associated ophthalmopathy (TAO) and controls using impression cytology technique. 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. 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. 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.