Intonation weirdness

I’ve always checked my intonation using the 12th fret harmonic. But today I checked it with the fretted note and it’s a few cents flat.

That’s just weird. I am using the harmonic directly over the fret but when fretted it’s not the same pitch. I don’t get it. What’s going on? Some effect of the string bending?

I’m assuming I should use the fretted note for intonation and not the harmonic?


I think I know what you are talking about, @howard and I also think I have noticed it as well, but I want to wait until I get back to my basses in a few hours to see how they are faring or whether I can reproduce what you are experiencing.

One of my first thoughts, however, was: do you have a high action on that bass? Somehow I have a gut feeling (for whatever that’s worth) that it might be connected to action height…

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Nope, medium low at the moment. Could be lower but not high at all.

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Another theory: playing the harmonic, it’s the pure harmonic at the frequency you would expect. Playing the fretted note, there’s clearly more low end to the sound, and it’s picking up more of the actual tone of the instrument.

But that’s just a guess.

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Yes, maybe…

I just checked briefly with my basses (and my tuner is probably not as good as yours), and ALL fretted notes at the 12th fret are sharp compared to the harmonics there. I had never noticed… but as you said, the harmonics are “purer”, while the fretted notes contains lots of other contributing frequencies.

It is almost OK for the Yamaha, but worse for the P-copy and the Fender Jazz (which I had never had for adjustment or done any myself).

Not sure if this helps any!? (Your fretted notes were flat - did I get that right)? One thing to remember is that at the 12th fret the string is only half as long as it used to be and perhaps slight variations in length become more pronounced!?


I have read others saying theirs was sharp too but mine is definitely flat.

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If you normally check your intonation using the open string and the 12th fret harmonic… you aren’t really checking your intonation because you are taking fretting out of the equation.

Intonation is basically compensation for how much you pull a string sharp by pressing it down to the fret. To set (or check) intonation, one of the notes you are comparing needs to be fretted. Common methods include comparing open/12th fretted or 12th fret harmonic/12th fretted or open/5th fretted/7th fretted (splitting the error between the 5th and 7th).


Got it, that makes sense - so it’t the relationship between the fretted note and the harmonic, not just the harmonic, and I need to shorten that particular string a little.



Yup @howard, you got it.


That worked great, sounds much better now too. E string was pretty far out of intonation. Thanks again!



If you don’t mind (and have the time), @howard : could you write up a short how-to (or: how-I-did-it)for us hardware challenged bassers?! (I still have plans for doing my first setup/adjustment during the Christmas break) :grinning:



Ditto Joerg’s request, @howard . . . :slight_smile:


As is obvious from the above I am not an intonation expert :slight_smile:

But it was really not too difficult, just a little time consuming. You might need a good tuner though.

Basically, what I did was repeat these steps. These will only work for basses with intonation screws on the back of the bridge for each saddle, which is common but not universal.

  1. Tune the open string.
  2. Play the 12th fret harmonic and fine-tune again if needed.
  3. Play the fretted note at the 12th fret.
  4. If the fretted note is flat compared to the harmonic, shorten the string by moving the bridge saddle closer to the headstock. On my bass, this means “loosen” the intonation screw for that saddle. This may be different on your bass. Take care not to loosen too much if your saddle is near the end of the screw.
  5. If the fretted note is sharp, move the bridge saddle away from the headstock. On my bass, this means “tighten” the intonation screw. I recommend detuning the string before you do this to ease tension on the intonation screw.
  6. Tune back up (important, changing the intonation will also change the tuning a bit) and repeat until the string is intonated correctly.

It turns out Marcelo has a video about this too, which I should have searched for before asking at all. He explains it all really well.

His other setup video is fantastic too, do it first before intonation:

Basically, to set up the bass, you want to do things in this order:

  1. Adjust truss rod if needed
  2. Adjust action if you want
  3. Set intonation if it is off

Thanks , Howard! That is what I call community service (I know it usually means something else, though…) :smile:

Much appreciated!