It's a medical term that comes, as so many of them do, from Greek.
It's a combination of two Greek words, idios, meaning "it's own" or "itself," and pathos, meaning "suffer." So the word literally means "it suffers by itself" or a bit more colloquially, "it doesn't come from anywhere else."
It means that this happens and we don't think that it has an external cause.
Sick sinus syndrome
, a disease of the sinus node, the heart's natural pacemaker, where it begins to degenerate for no known reason, is an example of an "idiopathic" disease or condition. It just happens and we don't know why.