Mitochondrial dysfunction occurs when the mitochondria do not work as well as they should due to another disease or condition. Many conditions can lead to secondary mitochondrial dysfunction including autism, Parkinson’s disease, Alzheimer’s disease, muscular dystrophy, Lou Gehrig’s disease, diabetes, and cancer.itochondrial dysfunction occurs when the mitochondria do not work as well as they should due to another disease or condition. Many conditions can lead to secondary mitochondrial dysfunction including autism, Parkinson’s disease, Alzheimer’s disease, muscular dystrophy, Lou Gehrig’s disease, diabetes, and cancer.