Purpose: To compare the inhibitory effects of dexamethasone and heparin on the infiltration of mast cells in the conjunctiva by using a mouse allergic conjunctivitis model. Methods: 24 Balb/c mice were divided into four groups: allergy group (positive control), dexamethasone group, heparin group, and negative control group, as groups 1, 2, 3, and 4, respectively. Each group comprised 6 mice, and experimental allergic conjunctivitis was developed in groups 1, 2, and 3. The mice in group 2 were treated with topical 0.1% dexamethasone eye ointment, and the mice in group 3 were treated topically with 5,000 IU/ml standard heparin. Both dexamethasone and heparin were instilled once a day for 4 days. Hanks' balanced salt solution was dropped into both eyes of the mice in group 4 instead of dexamethasone or heparin. Eyeballs and eyelids were removed from the mice in all groups while one eye of each animal was used for histopathological, the other for molecular biological examination. Results: Mast cells, infiltrating the subconjunctival tissue, were significantly lower in group 2 (p < 0.0001), group 3 (p < 0.0001) and group 4 (p < 0.0001) when compared to group 1. Conclusions: Topical heparin could be a viable option in treating IgE-induced allergic eye disease since it is found to be as effective as topical dexamethasone in experimental acute allergic eye disease.