I have been out sick from work, returing with very non-descript doctor's note. At this time, my illness is very personal and the doctor said that he does not (or can not) tell my employer exactly what is wrong with me. My question is, do i have to tell him what's wrong? I think that eventually i will, but in the testing/not sure stages, I don't feel that it is any of the company's business. Any advice?

Your employer is entitled to enough information to know whether or not FMLA protections apply (assuming that you and your employer both qualify for FMLA). That does not necessarily mean a full prognosis or even diagnosis, but "Nutmeg was seen in my office today" is not enough either.