Trachoma is a chronic keratoconjunctivitis caused by recurrent episodes of infection with the gram negative bacterium Chlamydia trachomatis. It is the most common infectious cause of blindness with at least 1.3 million estimated to be blind from the disease, 8 million to have trichiasis and 40 million to have active disease. Trachoma is now predominantly found in poor, rural areas in developing countries and it is classified by the World Health Organization as a Neglected Tropical Disease. Ocular infection with C. trachomatis is usually found in children and causes a marked inflammatory response with a follicular conjunctivitis and papillary hypertrophy. After suffering recurrent episodes of infection and inflammation these children are at risk of developing conjunctival scarring which can progress to entropion, trichiasis, corneal opacity and blindness in later life. The pathogenesis of the scarring process is believed to be immune mediated but is poorly understood. The aim of this work was to further our understanding of the pathogenesis of scarring trachoma. Two case-control studies were undertaken. The Trachomatous Scarring (TS) study included 363 cases with mild-moderate conjunctival scarring and 363 control subjects. Participants underwent a clinical examination, digital photography, in vivo confocal microscopy (IVCM) and had conjunctival swabs taken for quantitative gene expression, C. trachomatis detection and bacteriological culture. The Trachomatous Trichiasis (TT) study included 34 cases with trachomatous trichiasis who had severe conjunctival scarring and 33 control subjects. Participants underwent similar examination and sample collection procedures as those in the TS study, but in addition had conjunctival biopsy samples taken for histology and immunohistochemistry. Scarring was associated with evidence of an innate immune response with increased expression of antimicrobial peptides and pro-inflammatory mediators. Confirmation of an innate response was seen with immunohistochemistry with an increased infiltrate of Natural Killer cells seen in scarred tissue. Immunohistochemistry also showed an infiltrate of unidentified CD45 negative cells in cases. Scarring was associated with differential regulation of various modifiers of the extra-cellular matrix. There was no evidence of a Th2 response in scarred cases, but rather a Th1 response was detected. Non-chlamydial bacterial infection was more frequently found in cases than controls and was also associated with upregulation of innate and pro-inflammatory mediators. C. trachomatis was very rarely detected, but when seen was associated with a characteristic Th1 response seen in children. Connective tissue scarring could be seen morphologically with masked grading of IVCM and histological sections. An increased inflammatory cell infiltrate could also be seen with both examination techniques. Gene expression changes in relation to IVCM scarring generally showed good agreement with corresponding changes by clinical scarring. IVCM appeared to be able to detect subclinical scarring and also identified dendritifrom cells which were strongly associated with the presence of scarring. This work confirms other studies highlighting the importance of innate immune responses in the pathogenesis of trachomatous scarring. Non-chlamydial bacterial infection may be an important factor in driving this innate response with resulting tissue damage and fibrosis. Tissue changes could be objectively assessed with IVCM for various parameters, especially connective tissue scarring, and allowed some novel observations about the scarring process to be made.