I also had this diagnosed recently. My AME deferred my medical last fall. This was based upon an EKG and stress test, tread mill and nuclear. After the EKG, I had an echo-cardiogram, a heart catheterization, a cardiac MRI and this where things got interesting.

My cardiologist sent the findings to a colleague in Minnesota at the Mayo Clinic. He wanted to know how much scarring there was. This question got kicked to the people who did the cardiac MRI. Their response was "less than 15%." I also had genetic testing done which indicated my diagnosis wasn't due to any genetic anomalies. This information, combined with what the cardiologist and his staff were telling me, made me wonder.

Through an acquaintance, I was referred to the Cleveland Clinic. The Cleveland Clinic cardiology department has a VERY informative web site with lots of information on hypertrophic cardiomyopathy (HCM). I got an appointment and went through additional testing last month. According to them, I don't have HCM but a non-fatal condition which can lead to a false report on an EKG indicating HCM.

Now, my paperwork for a special issuance medical is at the FAA in OKC or is in Washington, D.C. As an ALPA member, I'm using Aviation Medical Advisory Service (AMAS) and their staff has been excellent.