Numerous studies have demonstrated that topical medications and preservatives used for the management of glaucoma can induce significant histopathologic and inflammatory changes in the ocular surface. This study describes an increased expression of major histocompatibility complex class II antigen HLA-DR, used as a marker of inflammation, on conjunctival epithelial cells in patients treated with multiple BAK-preserved topical glaucoma medications, confirming the presence of conjunctival inflammation. This increase in HLA-DR expression correlated with an increase in extracellular metalloproteinase inducer (EMMPRIN) membrane expression. EMMPRIN has been shown to stimulate the production of several matrix metalloproteinases (MMP) in pathological situations such as corneal ulcers and dry eye. This study suggests an MMP mediated modification of the conjunctival extracellular matrix remodelling in glaucoma patients using multiple eye drops with BAK preservative. This is not only important in the symptoms patients experience, which can affect compliance but also has an impact on future management with glaucoma filtration surgery as conjunctival wound healing is a major determinant for its success.