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Visual system is at high risk of iatrogenic damage. Laser ocular surgery, the use of powerful illumination devices in diagnostics and surgical treatment of eye diseases, as well as long surgeries under general anesthesia provoke the development of chronic degenerative changes in eye tissues, primarily in the cornea and the retina. Despite the existence of approaches for prevention and treatment of these complications, the efficacy of these approaches is often limited. Here, we review the mechanisms of iatrogenic damage to eye tissues at the cellular and biochemical levels. It is well recognized that oxidative stress is one of the main factors hindering regeneration of eye tissues after injuries and, thereby, aggravating iatrogenic eye disorders. It is accompanied by the downregulation of low–molecular–weight antioxidants and antioxidant enzymes, as well as changes in the expression and redox status of proteins in the damaged tissue. In this regard, antioxidant therapy, in particular, the use of highly effective mitochondria–targeted antioxidants such as SkQ1, is considered as a promising approach to the prevention of iatrogenesis. Recent findings indicate that the most efficient protection of eye tissues from the iatrogenic injury is achieved by preventive use of these antioxidants. In addition to preventing corneal and retinal cell death induced by oxidative stress, SkQ1 contributes to the restoration of innate antioxidant defense of these tissues and suppresses local inflammatory response. Since the timing of routine medical manipulations is usually known in advance, iatrogenic damage to the ocular tissues can be successfully prevented using mitochondria–targeted therapy.