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The conjunctiva forms a continuous mucosal surface from the eyelid margin to the cornea, and makes contact with airborne antigens and those on the adjacent eyelid skin and preocular tear film. Conjunctival lymphoid follicles (CLF) undergo hyperplasia upon conjunctival infection by a specific array of pathogens; infection-associated enlargement of draining preauricular lymph nodes suggests that CLF participate in the afferent limb of acquired immune responses for the ocular surface. In this review, we examine the evidence for classification of CLF as part of the common mucosal immune system, and explore the possible therapeutic implications.