Pain of any kind should be taken with caution until you gain experience in understanding how bad is bad - and you know your body. With experience you will know when you can continue to work through an injury or when you should back off.
It could be caused by a ton things and no one here or anywhere else (forum wise) can tell you "how" - "what" or "why" it is happening.
If your just starting out check out
http://forums.runnersworld.com
There are a ton of great runners that hang there, especially on the marathon forum - so over time it will be a great place to learn in the future. Maybe in time you may want to even become part of our mileage game.
A few thing to ponder -
1. Are you in the right shoes? The correct size? What type of shoe do you really need - are you a "stability", "cushion" or a "motion-control" runner? Are you running with the correct socks?
2. If it were me the first thing I would do is switch my shoes (I rotate between at least 4-different pairs of different types and different mfg's). daily so that I'm not runing in the same pair of shoes 2-days in a row.
3. Change your running surface (my daily run is no less than 9-miles but it is a good combination of hills, trail, blacktop, and concrete) to change things up enough and to place emphasis on various muscle groups.
4. Develop a "hard" - "easy" approach to your training
5. Change your training routine, in that you are not doing the same thing every day.
a. Change the distance of each run
b. Change the purpose of each training session (even when building base miles/time it's important for your body to gain experience within the various training zones)
6. One of the most useful things you can do is keep a runners/training log - recording such things as the distance (or specific loop), your time, the weather, your overall progress and any pains you may have or develop. I know when I'm due for a rest, a cutback day or wheather I'm "race ready" by the data in my daily training log.
Good luck