Purpose The purpose of this study was to assess the ability of quantitative in vivo confocal microscopy to characterize the natural history and detect changes in crystal volume in corneas from a novel animal model of cystinosis, the cystinosin (Ctns-/-) mouse. Methods Two Ctns−/− mice and one C57Bl/6 mouse were examined at each of the following time points: 2, 3, 5, 7, 10, 12, and 14 months of age. In vivo confocal microscopy scans were performed in 4 different regions of the cornea per eye. After, animals were sacrificed and cornea blocks evaluated for cell morphology using phalloidin and lymphocytic infiltration using CD45 antibodies by ex vivo confocal microscopy. Cystine crystal content in the cornea was measured by calculating the pixel intensity of the crystals divided by the stromal volume using Metamorph Image Processing Software. Results Corneal crystals were identified in Ctns−/− eyes beginning at 3 months of age and increased in density until 7–12 months, at which time animals begin to succumb to the disease and corneas become scarred and neovascularized. Older Ctns−/− mice (7 months and older) showed the presence of cell infiltrates that stained positively for CD45 associated with progressive keratocyte disruption. Finally, at 12 months of age, decreased cell density and endothelial distortion were detected. Conclusions Confocal microscopy identified corneal crystals starting at 3 month old Ctns−/− eyes. Cystine crystals induce inflammatory and immune response with aging associated with loss of keratocyte and endothelial cells. These findings suggest that the Ctns−/− mouse can be used as a model for developing and evaluating potential alternative therapies for corneal cystinosis.