Down syndrome (DS) is linked with mitochondrial dysfunction, which results in accumulation of damaged mitochondria. This study revealed that mitophagy, a form of selective autophagy activated to clear damaged mitochondria, is deficient in primary human fibroblasts derived from individuals with DS. This leads to accumulation of damaged mitochondria with consequent increases in oxidative stress. They identified that PINK1/PARKIN impairment and abnormal suppression of macroautophagy causes this mitophagy deficiency. The dataset includes RNA sequencing data. This study found that mammalian target of rapamycin (mTOR) is strongly hyperactivated, which suppresses macroautophagy induction and the transcriptional expression of proteins important for autophagosome formation.