We modified the conventional impression cytology technique for conjunctival study by designing a 24-well Teflon sample holder, using cellulose acetate paper cut in an asymmetrical shape, and introducing Gill's modified Papanicolaou stain. Using this modified technique, we studied 35 normal subjects and 67 patients with various ocular surface disorders, 42 of whom were later found to have squamous metaplasia. Six different cytological stages were defined based on changes of goblet cell density, nucleus, and cytoplasm, encompassing three major steps: (1) loss of goblet cells, (2) increase of cellular stratification or enlargement of superficial cells, and (3) keratinization. This staging system allowed us to correlate pathological changes with clinical findings, and to investigate the action mechanism of squamous metaplasia of conjunctival epithelium. This modified impression cytology technique may help increase understanding of various ocular surface disorders.