Haemopoietic Stem Cell Transplant (HSCT) is used as a treatment for a number of conditions particularly leukaemias. Following conditioning and HSCT, there is a ‘resetting’ of the immune system, which reconstitutes over a number of months. Graft-versus-Host Disease (GvHD) is a life-threatening complication of HSCT that includes severe, sight-threatening dry eye disease. In GvHD transplanted immune cells mount an immune response against the host. This thesis investigated how the immune cells of the conjunctiva are affected by HSCT and how the ocular surface leukocytes reconstitute. A non-invasive technique, ocular surface impression cytology (OSIC), was used to demonstrate that whilst there was no apparent depletion of innate immune cells in the conjunctiva, there was a marked reduction in the lymphocytes, which gradually reconstituted, returning to normal levels at the 6 months timepoint. Secondly OSIC was used to profile the leukocyte population in a cohort of patients post-HSCT with and without eye disease. In patients with dry eye disease following HSCT, the conjunctiva contained increased CD8+ lymphocytes, macrophages and neutrophils; a pattern that was distinct to that found in patients with dry eye disease following HSCT.