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When I was around 13 I had an ablation for an extra pathway in my heart that was making me black out during normal, everyday activities. After the ablation I still had flutters in my heart, and I went to my doctor and she told me that it is a completely normal feeling to have. The way she explained it to me is that since she technically "cut" the extra pathway, the electrical currents can still sometimes leap across the divide, but the procedure will always stop them in their tracks around a couple seconds into it. I'm assuming this is the same feeling you're having since you're saying "flutters" and not "fast heart beat." I've actually come to appreciate what the flutters are telling me about my body. It acts like an early warning system if my body is stressed, like if I'm tired, dehydrated, stressed or getting sick. This way I know I'm doing a little too much and need to take a couple second breather before diving back into life. Usually I'll just drink some water or eat a little healthier to get a better vitamin intake and they will stop. I also never let it stop me from doing the things that I want to do. I say this because it sounds like it's stopping you from living life. I have flutters all the time and I still have managed to play sports up to the college level, run 5ks and half marathons and live an all around healthy life all without any supporting medications. I'm obviously not a doctor, but if your doctor says to not worry too much about it I would believe him, since he's probably done over a hundred of these procedures throughout his career. Sometimes the process of worrying is more of the issue than the actual problem itself. So I guess the answer to your question, with my experience, is no, the flutters will not stop, but they are also not hurting you. In fact, they are actually a good indicator of your bodily state, and if you learn how to listen to them you actually have a one-up on the rest of the population who has never had to deal with what you're going through. I hope this helped you out a little : )
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