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In recent years, increasing consideration has been paid to the role of autophagy\u2014the cellular mechanism for the degradation and recycling of intracellular components in the pathogenesis of mitochondrial diseases. This review synthesizes current knowledge on molecular mechanisms of macroautophagy and selective forms of au-tophagy targeting specific organelles and structures: mitophagy, pexophagy, ribophagy, ER-phagy, aggrephagy, lipophagy, lisophagy, and nucleophagy. Using classic mitochondrial syndromes\u2014Kearns\u2013Sayre syndrome (KSS), MERRF, and MELAS, as well as various mitochondrial myopathies\u2014as examples, we discuss experimental evidence indicating both compensatory activation of autophagy and its insufficiency or blockade at different stages. Furthermore, we examine the link between deficiencies of key fatty acid \u03b2-oxidation enzymes (VLCAD, MCAD, CPT2) and impaired autophagic flux, including secondary defects of mitophagy mediated by energy deficiency. The review systematises current understanding of how dysregulation of selective autophagy promotes the accumulation of damaged mitochondria, oxidative stress, inflammation, and cell death in mitochondrial diseases. Prospects for therapeutic modulation of autophagy as a potential approach to treating these disorders are discussed.<\/jats:p>","DOI":"10.3390\/cells15151371","type":"journal-article","created":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T17:01:46Z","timestamp":1785344506000},"page":"1371","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["The Role of Autophagy in the Pathogenesis of Mitochondrial Diseases"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8059-9743","authenticated-orcid":false,"given":"Elena D.","family":"Avdonina","sequence":"first","affiliation":[{"name":"Federal State Budgetary Scientific Institution Research Centre of Medical Genetic, 1 Moskvorechye St., Moscow 115522, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergey I.","family":"Kutsev","sequence":"additional","affiliation":[{"name":"Federal State Budgetary Scientific Institution Research Centre of Medical Genetic, 1 Moskvorechye St., Moscow 115522, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aleksandr V.","family":"Shestopalov","sequence":"additional","affiliation":[{"name":"Federal State Budgetary Scientific Institution Research Centre of Medical Genetic, 1 Moskvorechye St., Moscow 115522, Russia"},{"name":"Department of Biochemistry and Molecular Biology, Pirogov Russian National Research Medical University, 1 bldg. 6 Ostrovityanova Ulitsa, Moscow 117513, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1159\/000446586","article-title":"Primary Mitochondrial Disease and Secondary Mitochondrial Dysfunction: Importance of Distinction for Diagnosis and Treatment","volume":"7","author":"Niyazov","year":"2016","journal-title":"Mol. 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