When playing my guitar, some notes are out of tune, even though the open notes are tuned properly.
Intonation is not adjusted properly. A lot of factors affect intonation. The intonation of a guitar is basically how accurate the tuning of the guitar is as you work up the neck. Your 12th Fret is the octave of your open notes. This is exactly 1/2 of the distance from your nut to where your strings rest on the bridge. Or at least it should be! Your higher notes will be off if this distance is off. The bridge of most electric guitars has an adjustment to move the resting point of each string closer or farther from the head of the guitar. This is how we ajust the intonation.
I am going to assume for this post that your neck is strait, and your stings are set to the proper height to avoid high action or buzzing. Your neck truss rod adjustments and string height (Action) should be adjusted before working on your intonation. See the respective articles for these adjustments.
Start by tuning your open notes. (See Part 1 blog for putting graphite in your nut)
You should use a tuner for this, as you want to be extremely acurate. (Make sure to be exact, or it will throw off the rest of this.)
Now we are going to check the tuning on the 12th fret. Make sure not to bend the strings up or down while doing this, only push strait in.
If your 12th fret is perfectly in tune, your intonation should already be correct.
If it is out of tune, try moving the adjustment at the bridge for that string a little closer to the neck of the guitar via the screw style adjustment. Take note of whether the note is sharp or flat, and by how much approximately.
Next, you need to tune your open note again.
Then check the tuning of the 12th fret.
If it is closer to being in tune, you are moving in the correct direction.
If it is farther out of tune, you went the wrong way - go the other direction.
Tune the open note.
Check the 12th fret tuning.
Repeat this process until the 12th fret is in tune.
Repeat this for all strings.
Assuming your neck is properly made, and not bowed... You should be in tune with yourself in a matter of minutes. :)