After returning from the Beagle in 1836, Charles Darwin suffered for over 40 years from long bouts of vomiting, gut pain, headaches, severe tiredness, skin problems, and depression. Twenty doctors failed to treat him. Many books and papers have explained Darwin's mystery illness as organic or psychosomatic, including arsenic poisoning, Chagas' disease, multiple allergy, hypochondria, or bereavement syndrome. None stand up to full scrutiny. His medical history shows he had an organic problem, exacerbated by depression. Here we show that all Darwin's symptoms match systemic lactose intolerance. Vomiting and gut problems showed up two to three hours after a meal, the time it takes for lactose to reach the large intestine. His family history shows a major inherited component, as with genetically predisposed hypolactasia. Darwin only got better when, by chance, he stopped taking milk and cream. Darwin's illness highlights something else he missed—the importance of lactose in mammalian and human evolution.