Although apoptosis is equally important both for the development and for the maintenance of homeostasis in some adult tissues, it can also be associated with disease processes. Current studies indicate that apoptosis is a mechanism of cell death in several important ocular and gastrointestinal diseases including glaucoma, and Helicobacter pylori (H. pylori)-induced upper gastrointestinal disorders and/or extraintestinal diseases, including autoimmune and neurodegenerative ones (Sjögren's syndrome, Guillain-Barre syndrome or Parkinson's disease). Glaucoma is also associated with similar autoimmune and neurodegenerative disorders, characterized by apoptotic loss of specific populations of neurons. Recently, a high prevalence of H. pylori infection has been recognized in patients with chronic open-angle glaucoma. In addition, H. pylori eradication may positively influence glaucoma parameters, thereby suggesting a possible causal link between H. pylori and glaucoma. H. pylori infection may influence the pathophysiology of glaucoma by releasing various proinflammatory and vasoactive substances, as well as by influencing apoptotic process; parameters that may also exert their own effects in the induction and/or progression of glaucomatous neuropathy. Importantly, H. pylori infection and glaucoma share the Fas/FasL and the mitochondria-mediated apoptotic pathways, thereby proposing an apoptotic link in the pathophysiology of both diseases.