OBJECTIVE: To compare conjunctival staining between lissamine green and fluorescein sodium using a yellow barrier filter. DESIGN: Retrospective cross-sectional study. PARTICIPANTS: Thirteen eyes of 13 patients with dry eyes. METHODS: All patients underwent ocular surface staining with fluorescein sodium and lissamine green. Ocular surface staining with fluorescein sodium was observed through slit-lamp examination under cobalt blue illumination and a yellow filter. Temporal (0-5) and nasal (0-5) conjunctival staining grade was separately graded according to the Oxford scheme. The contrast score was defined as the absolute difference between mean grey values of punctate staining and background. Conjunctival staining grade and contrast scores were compared between these 2 staining methods. RESULTS: The sum of the conjunctival staining grade (0-10) for the nasal and temporal conjunctiva was 4.7 ± 2.5 for fluorescein sodium, which was significantly higher than that of lissamine green, 4.1 ± 2.5 (p = 0.005). The contrast score of temporal and nasal conjunctival staining was 34.6 ± 12.0 and 34.7 ± 10.3, respectively, for fluorescein sodium, which was also significantly greater than for lissamine green (23.4 ± 8.1 and 21.0 ± 9.0, respectively; p = 0.003 and p = 0.003, respectively). CONCLUSIONS: Conjunctival staining with fluorescein sodium and a yellow filter seems to be more sensitive for the detection of conjunctival damage than lissamine green. Fluorescein staining with the yellow filter has the advantage of simultaneous observation of both corneal and conjunctival damage in patients with dry eye without the need for additional vital staining.