I have had this problem in the past but I've managed to mostly get over it. I don't know if my techniques will help anyone else, but here are my suggestions:
1) I realized that I was mostly afraid of dying, and that I would die of something I could have prevented if I had gotten care earlier. I realized I was afraid of the guilt of dying (and the hardship it would be for my family, etc.) So one of the most important things for me -- and I know it sounds bizarre - was to give myself permission to die of something I didn't catch. I decided I wouldn't blame the people I care about if something like that happened, so I forgave myself preventatively. The other oddly helpful thought was "It's not the end of the world if I die." It might be the end of my world, but other people would get through it.
2) Learn to laugh at yourself. I often think of "my brain" as something separate from me, so when my fingers tingle and I think I'm having a stroke, I immediately make fun of my brain for overreacting. Sometimes I congratulate it for being so clever - it can really come up with some interesting stuff.
3) Don't run to the doctor every time something doesn't seem right. They are trained more to deal with physical than psychological stuff, so they'll take you at your word and then they're legitimizing your fears. Of course you should go to a doctor if you're really sick, but either ask someone else's advice (and take it!) or try the next step.
4) Set a time limit. Tell yourself you're not in the right frame of mind to make health judgments now, and you'll write it down and think about it more in an hour (or a week, depending on the type of thing you think is wrong with you). By that time you'll probably be calmer and it will probably be gone.
5) DO NOT watch Grey's Anatomy, House, E.R., or any other medical show. They find the most dramatic diseases they can. Real doctors spend almost all of their time on a very short list of very common ailments, not solving medical mysteries (like why you have an eye twitch and stomach pains). Likewise, don't read those "Is it a headache or imminent death?" articles in magazines. Women, Redbook is a particularly bad one for us.
6) Realize that sometimes you're using magical thinking. If it seems very dramatic or mysterious or rare, it's probably not true -- it's just a good plot for a TV show. Real life is not fair and it's often very boring.
7) If your doctor says you're ok, take your chances and trust them. (Of course there are times when you should get a second opinion, but if you know you're a hypochondriac you also need to realize that if you can convince yourself the first doctor was missing something, you can convince yourself of the same thing about the second, third, fourth.)
8)If it's something you've had before and you were fine then, you're almost certainly fine now.
9)Stress and anxiety can cause almost any physical symptom, including visible ones (like hives). Assume that it's stress and see if you can make it go away over time by calming down (don't monitor it constantly, though).
10)Learn to trust your body (hard to do; I don't have this one down yet). If you're REALLY, REALLY sick, you'll know it. Let yourself off the hook on the early detection stuff.
The hardest thing about it is the "what if" factor -- what if you're wrong and it really is Disease X? That's when you just have to try to accept that there is uncertainty in life. Think of something you honestly don't worry about, like being attacked by an escaped zoo animal. You can get on with your life taking the chance that a stray lion could eat you, so you can accept that there is an incredibly small chance that you really do have Disease X.
This is not medical advice - just my own experience. Please don't sue me.
. I was a fearful, anxious wreck. Fortunately I was able to get in a health-anxiety program--free, even better--and got a hold of my anxiety.