Intonation is the accuracy of your guitars pitch all the way down the neck. It is relative to each individual fret. If your intonation is correct then when you play the lowest string on your guitar (an E) then each fret up should be perfectly in tune: E (open), F (1st fret), F sharp (2nd fret) G (3rd fret) and so on. If your intonation is right then all the other notes on your guitar will be perfectly in tune with your open string. Intonation doesn’t always go askew on all frets; it’s usually only a few here and there and gets worst if not attended to.
If you want your guitar to sound good then you need to keep your guitar properly intonated so it is in relative tune to itself. Generally you should check your intonation every week or so, just to make sure that your guitar is sounding as good as it can. To check your intonation you need a tuner and you should do one string at a time. The procedure for checking your intonation is as follows.
1. Turn on your tuner and tune the string to the right pitch.
2. Strike the 12th fret harmonic; make sure it is tune with the open string. (they should be the same note).
3. Now strike the note at the 12th fret (not the harmonic) all three of these notes should be the same note. If they are, then your intonation if probably fine if not then you could have a serious problem.
If you have a problem with your intonation then you should take your guitar to the nearest guitar store and get a professional to fix it for you.
Good luck with your practice!
Posted by Ben Edwards