This is called delayed onset muscle soreness (we call it DOMS). I don’t think scientist truly understand how this work but I may be wrong. Mostly we think it is to do with damage to the muscle during exercise. Every time you exercise hard you damage your muscles and then they repair and get bigger or better at doing that type of exercise. I think you mostly get DOMS if you do unfamiliar exercise. for example if you run down hill for a long time you will be in pain for days. I remember the first time I ran down Snowdon, I couldn’t walk for a week. but if you do it again and again your muscles will adapt and get use to it.
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