It has been suggested that epigenetic modifications involved in the expression of disease-related molecules may be important for familial Parkinsonism caused by a single gene as well as sporadic disease. On the other hand, epigenetic modification has been shown to be induced by various stimuli such as infection, inflammation, stress and aging. Epigenetic modification is known to involve intracellular metabolites, and dysregulation of the metabolism can lead to changes in mitochondrial function, metabolites, and nutrient-sensing pathways, and directly affects epigenetic regulation of gene expression, such as histone and DNA modification. Our recent studies have shown changes in the glycolytic and methionine cycles in dopamine neurons derived from iPS cells in patients with familial Parkinson's disease. Under these conditions, we also found a significant increase in dopamine-metabolizing enzyme expression in dopaminergic neurons along with epigenetic modifications including DNA hypomethylation. These findings suggest that intracellular metabolism may be involved in changes in gene expression associated with epigenetic modification in dopamine neurons derived from iPS cells in patients with Parkinson's disease.