Compounds, compositions and methods are provided for mitochondrial modulation. The subject mitochondrial modulator compounds generally include a head group linked to a charged moiety. In certain cases, the head group is a heterocyclic or a heteroaryl group. Aspects of the subject methods include a method of modulating mitochondria. Aspects of the subject methods include treating a subject having a metabolic syndrome-related disease or a symptom thereof by administering to the subject a therapeutically effective amount of a subject compound. In certain cases, the disease is selected from hyperlipidemia, type 2 diabetes, fatty liver disease, obesity, cardiovascular disease and stroke. In certain cases, the symptom is selected from abdominal obesity, insulin resistance, hyperinsulinemia, high levels of blood fats, increased blood pressure, and elevated serum lipids.