Sounds like the intonation is out. If it is an acoustic the neck may be bowed. If it is an electric and an adjustable bridge you may try the following. Found this process I use @ http://en.wikibooks.org/wiki/Guitar/Adj … the_Guitar
Adjusting intonation
You may notice each string on the bridge sits in a "saddle".
Depending on your setup, you might notice the saddles may be in different positions:
some might be pushed forward and others might be pushed back,
sometimes slightly. The positioning of the saddle effectively
changes the length of the vibrating string. Tune the guitar
to concert pitch with the aid of an electronic tuner,
making sure the open strings are perfectly in tune.
Play the 9th and 12th fret harmonics, then play the fretted notes.
If the fretted notes are sharp, the string is too short and the saddle needs
to be pushed back toward the base of the bridge.
If the note is flat, the string is too long and the saddle needs to be pushed up
toward the nut. Repeat this procedure for each string.
Adjusting the intonation should be done every few months or at least twice a year.
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