The guitar can be played in many positions, but some positions are clearly more efficient than others. The choice of position is personal, but clear guidelines exist. Some basic considerations in determining a chosen playing position include:

• the physical stability of the instrument
• ensuring the freedom of both hands such that they have thorough access to the instrument and can meet all technical demands without having to support the instrument
• elimination of general muscular tension in the assumed body position. While it is natural for a beginner to experience fatigue in the muscles of his hands and arms, you must be careful to sit straight and not cause damage to your spine and waist. If you do experience pain in those regions it is possible that the position is harmful and must be changed to prevent damage.

Many beginners try and turn the guitar towards themselves, so they can look down at the frets and soundhole. Curling the guitar towards yourself in such a way actually makes it more difficult to fret the strings efficiently, because you have to curl your wrist more. This tension can be harmful. Beginners are also often inclined to put their elbow too high or low, which leads to cramping. Ideally your arm and shoulder should be relaxed.
It may take a beginner several weeks until holding the guitar feels comfortable and natural. By using efficient hand positions and not straining, the muscles in the arm and hands will get stronger. If you ever feel pain you should immediately stop and ascertain the cause of pain before continuing. Sometimes discomfort is due merely to fatigue and a period of rest will be all that is required.

Content Credit: http://en.wikibooks.org/wiki/Guitar/The_Basics