Macrophages infiltrate the conjunctiva in severe cases of allergic conjunctivitis (AC) such as atopic keratoconjunctivitis (AKC). We established experimental immune-mediated blepharoconjunctivitis (EC) in Brown Norway (BN) rats as a model for severe types of AC. We investigated whether macrophage infiltration in the conjunctiva in this EC model is inhibited by clodronate liposomes (CL2MDP-lip). The numbers of ED1-positive but not ED2-positive macrophages in the conjunctivas were increased by the induction of EC. Subconjunctival injection of CL2MDP-lip decreased the number of ED2-positive but not ED1-positive macrophages in the conjunctivas of naive rats. CL2MDP-lip did not affect macrophages in the spleen. Subconjunctival injection of CL2MDP-lip into EC-developing BN rats decreased the number of ED2-positive macrophages at all the time points. ED1-positive cell infiltration was inhibited when treatment was administered just prior to OVA challenge. Intravenous injection of CL2MDP-lip decreased the number of ED2-positive cells in the conjunctiva. Thus, we conclude that CL2MDP-lip inhibits infiltration of macrophages into the conjunctiva within 24 h of antigen challenge.