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Techniques outlined in this article include qRT\u2010PCR, immunoblotting, immunofluorescence, transmission electron microscopy, Seahorse bioanalysis, staining for mitochondrial membrane potential, detection of mitophagy, and mitochondrial functional assays. Most of these techniques have been performed <jats:italic>in vitro<\/jats:italic> (in human and mouse neuronal cell lines transfected with mutant amyloid precursor protein or tau protein cDNAs) and <jats:italic>in vivo<\/jats:italic> (in brain tissues from different mouse models of Alzheimer's and other neurological diseases). Mitochondrial abnormalities in Alzheimer's disease have taken various forms, including excessive reactive oxygen species production, mitochondrial calcium dyshomeostasis, loss of ATP, defects in mitochondrial dynamics and transport, and mitophagy. Mitochondrial dysfunction is largely involved in aging; age\u2010related diseases such as cancer, diabetes, and obesity; and neurodegenerative disorders including Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, multiple sclerosis, and others. The goal of this article is to make protocols\/methods available to students, scholars, and researchers of mitochondria in order to facilitate future mitochondrial studies. \u00a9 2023 Wiley Periodicals LLC.<\/jats:p><jats:p><jats:bold>Basic Protocol 1<\/jats:bold>: Analyzing mitochondrial gene expression in mouse brain tissue and HT22 cells by qRT\u2010PCR<\/jats:p><jats:p><jats:bold>Basic Protocol 2<\/jats:bold>: Analyzing protein expression in mouse brain tissue and HT22 cells by immunoblotting<\/jats:p><jats:p><jats:bold>Basic Protocol 3<\/jats:bold>: Immunofluorescence staining of cells and tissue sections<\/jats:p><jats:p><jats:bold>Basic Protocol 4<\/jats:bold>: Staining for mitochondrial membrane potential<\/jats:p><jats:p><jats:bold>Basic Protocol 5<\/jats:bold>: Assessing mitochondrial structure by transmission electron microscopy<\/jats:p><jats:p><jats:bold>Basic Protocol 6<\/jats:bold>: Methods for detecting mitophagy<\/jats:p><jats:p><jats:bold>Basic Protocol 7<\/jats:bold>: Bioenergetics assay via Seahorse<\/jats:p><jats:p><jats:bold>Basic Protocol 8<\/jats:bold>: Assays for mitochondrial function<\/jats:p>","DOI":"10.1002\/cpz1.631","type":"journal-article","created":{"date-parts":[[2023,1,17]],"date-time":"2023-01-17T14:31:15Z","timestamp":1673965875000},"source":"Crossref","is-referenced-by-count":10,"title":["Methods to Study Mitochondria: Techniques Used to Study the Effects of Age\u2010Related Diseases Including Alzheimer's"],"prefix":"10.1002","volume":"3","author":[{"given":"Javaria","family":"Baig","sequence":"first","affiliation":[{"name":"Department of Internal Medicine Texas Tech University Health Sciences Center  Lubbock Texas"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jangampalli Adi","family":"Pradeepkiran","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine Texas Tech University Health Sciences Center  Lubbock Texas"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P. 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