The integrity and assay performance of tissue mitochondrial DNA is considerably affected by choice of isolation method

•The procedure chosen for isolation of mtDNA from solid tissues has a considerable effect on the integrity of the product, as routine isolation methods yield mtDNA with numerous single-stranded nicks per mtDNA strand.•Modifications that benefit mtDNA integrity are made to the standard total DNA isolation procedure.•Four different DNA isolation methods are systematically compared with regard to the integrity of the resulting mtDNA, yield, mtDNA enrichment and labor.•We show that the choice of isolation method affects the performance of the mtDNA in downstream analyses such as long-range quantitative PCR.