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I've been working on my own workout structure for sometime now, trying to find the right combination of warm ups and exercises.

I always begin with a warm up, working on the muscles I'll be hitting that session.

Then I move on to the exercises I need to be freshest for, eg. any sort of jumps, box jumps etc.

Then I'll work on resistance exercises, finishing with treadmill or bike work.

Is there any scientific theory behind constructing workouts in the right order?

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Among many powerlifters, the theory is that you should try to warm up very little. Warmups are simply tests to spot joint or technique problems that could cause injury at full weight. Anything more is needlessly tiring yourself out before you can get to the heavy lifts that really increase strength.

Intuitively you would expect to lift the most weight in your first set since you are the freshest, the next most weight in your second set, and so on. Also intuitively, if you were to apply your lifts to the "real world" you may not get to warm up.

If you must combine cardio and strength training into one workout, then do the strength training first as you need to be fresh for heavy lifts, and not for cardio.

Note: I'm assuming that you are lifting for strength and doing cardio for heart health. If you're training to become e.g. a competitive runner then this may not be the right advice.

I think I would save stretching for the end of your workout, unless you are very tight, and don't overdo it.

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The theory is, there should be no set order. You need to mix things up - not only the exercises you are doing, but the order in which you are doing them. My philosophy is "never do the same exercises twice". This obviously doesn't work if your exercise is running or biking, but you can always choose a different route. If you are weight lifting then mix it up EVERY time you go to the gym. Gains are attained by challenging your muscles. If you do the same thing day in and day out your muscles will get use to it and you'll stop gaining.

That being said, you should warm up at the beginning and probably stretch at the end. Warm up on the exercise you are going to do first with lighter weight. Add two extra sets at the beginning to work yourself up to the working sets with the real weight.

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    If there is exercise science, coaching material, or really any reference that could back up your assertion that one should switch exercises and workout order in each training session, please provide it. Otherwise this seems absurd to me: virtually every coach, trainee and researcher has found clear evidence that ordering your workouts is more safe and productive than randomizing them. – Dave Liepmann Aug 24 '11 at 2:39
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    @DaveLiepmann, It appears that in this article here: bodybuilding.com/fun/arnold_arm_secrets.htm, it quotes Arnold recommending what Sparfusile mentions in the above answer. – Philoxopher Dec 7 '12 at 10:39
  • @KerxPhilo The paragraphs under "shock the muscles into change" definitely encourage changing up one's training, but Sparafusile advocates switching up the exercises every workout, and explicitly rejects any ordering within a workout. If his wording was hyperbolic and he agrees with the bb.com article, we would be closer to agreement. – Dave Liepmann Dec 7 '12 at 14:09

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