Stretching is an important part of most workout routines, running included. Unfortunately, stretching is the first thing that gets left out if you are in a hurry or you're trying to squeeze in your exercise for the day. You should be stretching before and after you run. Even five minutes of stretching before to warm up your muscles and five minutes of stretching after for a cooldown can prevent serious injury. I normally recommend 15-20 minutes of stretching to my patients before and after their workouts.
There are many different stretches. Regardless of which ones you choose to do, make sure you stretch into comfort and not pain. If a stretch is hurting, back off or don't do it. Pain is an indicator that something is wrong, and pushing past this point can invite injury to your door.
Since we all run at different paces, try the following protocol the next time you finish stretching. After stretching, begin walking at a slow, comfortable pace. After a few minutes, increase your pace gradually to a faster walk, then to a light jog and then into your full, usual running speed. Obviously, the time it takes you to get to a full run will vary, but it is a nice way of getting your body into the groove. Once you are almost finished with your run, gradually slowing your pace to a walk is a nice way to start your cooldown.