I moved my saddle as far as it can go towards the neck, and still the intonation is bad. Please do not write about moving saddles, because I did that. I would be grateful if you could tell me about other possible solutions.

It is a 0.009 string on a Yamaha Pacifica 112j. The string has been used for about 2 months daily. I can not take an exact measurement, but the action is for sure below 2mm, so I think it is not a problem there. I play guitar daily.

My nut is okay; I made a "capo" by placing my hand right on a fret and everything was good. I should say too that every other string is close to be perfect. I think in that kind of guitar, it's acceptable. I am interested in fixing the intonation of the thin E string, but to make sure or even thick the sort of things to check I mentioned it here.

I tryied to change action and set it higher and even lower, but it didn't repair anything, so i returned to one that i had before. The problem is appearing only on thin e.

I forgot to tell when the problem occured. I'm not sure but if i had to tell when it did, i would say after restringing.

On my eye neck is straight and radious looks well. Same with frets. However if there is any better method to figure out if the neck and frets are ok than by eye let me now then.

Olde leprechaun mentioned about checking intonation on 3rd fret and that one tunes lower than it should but first and second frets are ok.

  • 1
    E1 is a bit ambiguous. I guess you mean the thin E string. What guitar, what gauge string. What's the action like? We need more detail, please.
    – Tim
    Mar 12 at 12:18
  • Also please give us an idea how you are using the guitar. How often? What kind of strumming? Mar 12 at 13:21
  • Does "gradually goes flat" mean "The open string is in tune, but the higher on the fretboard you go, the flatter the pitch?" Please edit to clarify. Mar 12 at 13:38
  • 1
    Also, have you had this same issue with 2 different E strings?
    – Edward
    Mar 12 at 23:04
  • 1
    When you say "the action is for sure below 2mm", do you mean the high E string is less than 2 mm away from the 12th fret? It's possible for the action to be too low, perhaps that is causing some issues. If you really can't move the saddle closer to the neck then something else is wrong. If you're new to guitar setups, you'll either have to keep working on it until you figure it out or take it to a professional. Mar 13 at 2:11

5 Answers 5


If your intonation goes flat as you move up the fretboard and the saddle rider is as close to the neck as possible it is quite likely that either the bridge is off (or the neck is set into the wrong position) or that the nut is off (yes, this can also be the case). To check whether the nut is off you can try intonating with a capo at the first fret, and then check intonation without capo. If the intonation is off the nut is likely misplaced.

Has the guitar had this problem since the beginning, or did this start later at some point? Considering this is a moderately cheap industrially made guitar with most likely a lack of QA I suppose there could be one or the other black sheep. If this only happened after some time it might be that the neck wood has bent or twisted a bit, which can happen especially on cheaper instruments where the wood might not be dried perfectly.

To fix a misplaced nut you’d need to have a nut fitted that compensates for that misplacement. To fix a misplaced bridge you’d need to either have the saddle reseated or try to change to a bridge that allows for more space for intonation.

If your action is quite low you could try raising it a bit. The higher the action is, the more the string will stretch on fretting, making the note sharper. But if you cannot get reasonable intonation out of the guitar with a normal setup you will most likely need a professional to fix saddle and/or nut.

If you bought this guitar recently you might very well be able to have it replaced, as it would likely have a construction problem.


I get this issue often with an old string. Particularly B and (thin) E. And especially if they are thin gauges (such as .009).

I don't know why this happens, my guess is that the string material loses tensile strength at some point. When the pitch change is noticeable, the string has been in use for at least a year (even if not played regularly), and it has lost its shine and turned dull in color (even though it's free from sweat deposits).

So, replacing the string fixes the issue. If however you have already put a new string on and you still have the same issue, then it's likely a structural problem as others have suggested. The first one I'd look at is the neck - if it's bending and the string distance from the neck increases noticeably as the pitch rises, that would be the likely cause. If the neck is ok, and the string is not too far from it even at the higher pitch frets, then it's time to look at the string length, nuts, frets, etc.

  • Is this possible that the string wore out after about 2 months daily playing if yes i'm going to change one and check if the problem disappear.
    – Bronko2321
    Mar 13 at 7:11
  • 1
    I'd say it's possible with a .009 in heavy use. Clear indication of this issue is that the intonation is correct when this string is new, and then as the time goes by, you start noticing it goes flat as you go up the fretboard. And the degree of flatness increases with time (provided your guitar setup remains the same - nuts, saddles, bridge, etc). If the intonation is wrong as soon as you put the new string on (after you've given it a day to stretch), then the problem would be something else (unless you got a bad quality string or a just bad batch, which is not very common nowadays).
    – aTreble
    Mar 13 at 22:11

aTreble has the right solution; replace the string. I've been fixing and building guitars for almost 30 years, and I didn't come across this problem until a few years ago. A customer brought me a MIM Strat that the high E was crazy flat at the 12th fret. I actually removed the adjustment screw and moved the saddle all the way to the pivot edge of the trem baseplate, and while it was closer to being in tune, it was still flat! All the other strings were fine, and their saddles were positioned as you'd expect, so it couldn't be the neck/frets/etc. otherwise it would affect neighboring strings to some degree. As far as I can figure, the string basically loses symmetry through wear, which affects how it vibrates (pitch) when you fret it higher and higher up the fingerboard. I've seen it a couple times since, and it's always been on old, worn strings, though I suppose it's possible to get a new string with a flaw from the factory that might have the same effect.


You've a priori elimated moving the saddle, but the symptoms suggest that the fretted string is progressively too long. If adjusting the saddle / bridge is out of the question, perhaps a thinner gauge E string would stretch (and therefore tighten) a bit more when pushed down to the fret, thus raising the pitch.

  • It works the other way round. The required stretch depends on the geometry but thicker string needs more force to stretch, increasing the tension and pitch more.
    – ojs
    Mar 12 at 17:05
  • @ojs The part you're missing is that pitch increases with the square root of tension. So, increasing a 20lb string to 21lb will have a larger effect on pitch than increasing a 30lb string to 31lb.
    – Edward
    Mar 12 at 23:00

Nut slot not deep enough, fretting is pulling the string too far down. Fret at 3 and check clearance of string to fret 1.

  • This makes the string go sharp, not flat.
    – Tim
    Mar 19 at 14:28

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