ABSTRACT Thirty‐one patients with the diagnosis of thyroid associated eye disease were included in the study. Samples were obtained from upper and temporal bulbar conjunctiva of both eyes by cellulose acetate filter paper. Control group included 20 healthy individuals. In patients with thyroid associated eye disease, grade 2 or 3 squamous metaplasia was observed in 32.26% of the samples obtained from upper bulbar conjunctiva, whereas this ratio increased to 82.26% in temporal bulbar area. None of the control cases showed changes of grade 2 or more. The evaluation of cytological changes with respect to clinical findings revealed that the main factor responsible for the cytological findings was inflammatory changes of the conjunctiva, whereas interpalpebral distance and proptosis had only a partial effect.