Hai, I'd be very grateful for any advice, this has appeared a few days ago and I've been trying to fix it without success:
The 3rd (G, or in my case, F# as I usually tune half step down) string is audibly sharp when fretted (tuner confirms) and it just won't intonate - the other strings are fine. I've been trying to adjust the bridge saddle, first moderately, and then even increasing length all the way and it seems it's pretty much identical regardless of how the bridge saddle is set. The bad intonation is not ear-splitting but it's definitely audible and sounds bad especially with arpeggios, and to put it bluntly it annoys the living **** out of me.

I find it fairly unlikely it's the strings' fault, they're Ernie Ball Cobalts (10-46) and not that old (2-3 weeks or so, and I haven't had time to play a lot recently so they're not really abused). The guitar is still fairly new (had it since March) and generally it's absolutely amazing - planning to take it to a luthier soon for a proper set-up, but I'd like to be able to fix this myself if possible for the moment.

Any ideas/suggestions? I'd be very grateful.
Make sure the nut is properly lubed. (Unless it's a locking nut)
Edit: I'm a moron. That's a tuning thing. Not intonation...Don't listen to me.
Last edited by GraceByDeath at Jul 11, 2015,
Actually, it might be the string's fault. The problem is that plain G strings are too thick making them stiff. As a result, G strings tend to be sharp across the frets on guitar and other fretted instruments with similarly wide plain strings, such as the G on a banjo. Non fretted instruments such as violins and steel guitars don't run into the same problem and as such can use thicker plain strings.

Some people suggest a wound G strings (the core of the wound G is thinner than a plain G and so it isn't as stiff despite being thicker) but the wound G is trickier to play, but that might be offset by your lower tuning.

A common solution is to make the G string slightly flat when playing in keys that don't heavily use the open G string (like A or E), particularly as the root note in a G chord, and then tune back up when playing in C or G.

Of course, that is assuming that there aren't any neck/bridge/nut related problems.
There's no such thing; there never was. Where I am going you cannot follow me now.
Looking at the nut is not a bad idea. If replaceable perhaps replace it and the saddle. There isn't much else to consider aside from the 12th fret itself at the level of the 3rd string.
If it's a tune-o-matic type bridge you can try turning the saddle around on the g string to gain a little extra adjustment(depending on which direction it's running out of adjustment).