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You need to stretch sometime AFTER your workout(it's also a good idea to eat protein in the first 30-40 mins after a workout because you absorb it faster). Your muscles are building up with lactate and other metabolites which is the cause of your muscle soreness.
Here is a very detailed article that explains it.
http://www.sciam.com...
Answer this Question: "Why am I in pain after exercising?"






Why am I in pain after exercising?
I am a wildland firefighter and it's the off-season and I'm laid off......so I need to stay in shape so I usually run, or uphill hike 3 miles in the morning for cardio, and then in the afternoon I usually do 3 sets of 50 push-ups and sits-ups.....but lately my back and hips hurt so much at the end of this that I can hardly bear the pain......but as soon as I wake up in the morning I feel great .....I was wondering, am I overdoing it or do I need cut back a bit or is it a part of my routine that I need to change?