Conjunctiva-associated lymphoid tissue (CALT) is a part of the eye-associated lymphoid tissue (EALT) at the ocular surface. Its lymphoid follicles are usually characterized by using light microscopy, but its ultrastructure remains largely unknown. In this study, flat whole-mount conjunctival tissues (n = 42) from 21 young adult rabbits were investigated native in reflected light, and further stained and cleared (n = 6), in paraffin histology sections (n = 6), scanning electron microscopy (SEM, n = 4) and transmission electron microscopy (TEM, n = 4). Secondary lymphoid follicles accumulated into a dense group nasally towards the lacrimal punctum of the lower lid. High endothelial venules (HEV) with typical ultrastructure occurred in the parafollicular zone. The bright germinal centre (GC) contained lymphoblasts, follicular dendritic cells, apoptotic cells and tingible body macrophages. The follicle-associated epithelium (FAE) was devoid of goblet cells and contained groups of lymphoid cells. TEM showed these cells to be located in cytoplasmic pockets of superficial electron-lucent cells with a thin cytoplasmic luminal lining that contained a fine filament meshwork and numerous endocytotic vesicles. These M-cells were sitting between and on top of the ordinary dense epithelial cells that were located basally and formed pillar-like structures. In stereoscopic SEM, the surface cells were very large, had a polygonal outline and covered cavernous spaces. The rabbit has a CALT with typical follicular morphology, including HEV for regulated lymphocyte migration and epithelial cells with ultrastructural characteristics of M-cells that allow antigen transport as indicated by the GC-reaction. The arrangement of these M-cells on top of and between epithelial pillar cells may reflect a special structural requirement of the multilayered CALT FAE.