Most cases of conjunctivitis may be categorized as either papillary or follicular, according to the macroscopic and microscopic appearance of the conjunctiva.

- Papillary conjunctivitis shows a cobblestone arrangement of flattened nodules with central vascular cores. It is most commonly associated with an allergic immune response, as in vernal and atopic keratoconjunctivitis, or it is a response to a foreign body such as a contact lens or ocular prosthesis. The histologic appearance of papillary conjunctivitis is identical, regardless of the cause: closely packed, flat-topped projections, with numerous eosinophils, lymphocytes, plasma cells, and mast cells in the stroma surrounding a central vascular channel.

- Follicular conjunctivitis is seen in a variety of conditions, including inflammation caused by pathogens such as viruses, atypical bacteria, and toxins (including topical medications). In contrast to papillae, follicles are small, dome-shaped nodules without a prominent central vessel. Histologically, a lymphoid follicle is situated in the subepithelial region and consists of a germinal center, containing immature, proliferating lymphocytes; and surrounding corona, containing mature lymphocytes and plasma cells. A follicle appears more pale on its surface and more red at its base (in contrast to papillae which are more red at the surface and pale at the base).