Specimens of a cornea, conjunctiva and iris were removed at the time of penetrating keratoplasty in a case of nephropathic cystinosis. Immunohistochemical studies revealed the presence of class II antigens on the stromal keratocytes of the cornea and the vascular endothelial cells, pericytes and fibroblasts of the conjunctiva. In addition, there were thinning and focal breaks in Bowman's membrane. Both of these findings may have contributed to the severe photophobia and blepharospasm seen in patients with longstanding cystinosis.