Well, as Dr. Ian puts it, "Because the stored fat is being used converted into ketones, you start losing weight and start dropping sizes, because you are reducing those fat cells." Other experts say the long-term accumulation of ketones could be harmful. “Those ketones are emergency fuel sources, and we’re not meant to run on them long-term,” says Kristen Kizer, a registered dietitian at Houston Methodist Hospital. “Ketones are negatively-charged molecules, which means they’re acidic. When you build up ketone bodies in your system, you’re building up acid.