Impression cytology was used to evaluate the conjunctival surface change after filtering surgery and its association with bleb type and mitomycin C. Impression cytology were obtained at least ten (mean, 20.4) months after surgery from 22 eyes of 19 patients who had undergone trabeculectomy, and were graded according to a previously described system. Blebs were divided into thin cystic and thick diffuse types. Abnormal impressions, demonstrated as disturbed epithelial and goblet cell morphology and a decrease in the numbers of both cells, were found in nine eyes (40.9%). With regard to the prevalence of abnormal impressions, there were statistically significant differences between bleb type and between the use or non-use of mitomycin C (p = 0.040, 0.013); these related more to the use of mitomycin C than to bleb type. This study reveals that filtering surgery causes long-term damage to the conjunctival epithelium overlying a filtering bleb, especially in a patient with a thin cystic bleb or one has been treated with mitomycin C. This change in the conjunctival surface may lead to the occurrence of late hypotony and bleb-related infection.