On the low e string, the open string and the e at the 12th fret are in tune but all the notes in between are sharp... how do I fix this? I thought it might just be the bow of the neck but I don't have this issue with any of the other strings (i don't think... my G string is sharp at the 12th fret but not this way)... how can i fix this?

What are you using as a tuner?

a Korg DT-10.

On the low e string, the open string and the e at the 12th fret are in tune but all the notes in between are sharp... how do I fix this? I thought it might just be the bow of the neck but I don't have this issue with any of the other strings (i don't think... my G string is sharp at the 12th fret but not this way)... how can i fix this?

You are fretting the 12th fret note, not just chiming the octave harmonic, right? If so, I don't know how this could happen unless it's supposed to have a zero fret and it's not there, maybe?

You've done this http://garywillis.com/pages/bass/bassmanual/intonation.html , but all the notes except for the open and 12th fret are off?

Are your strings new? Old strings can make weird things happen during intonation. If they are new, make sure you push down on the string around the saddles and the nut, to get the string to take the shape it eventually will anyway (get rid of that round hump over the saddle).
It's possible (but unlikely) that all the frets from 1-11 are off, in which case you're screwed, then you just have to find a happy medium where everything is kind of close.

You've done this http://garywillis.com/pages/bass/bassmanual/intonation.html , but all the notes except for the open and 12th fret are off?


Yes on the low e string... a little on the g string. the rest are okay. And i don't know how old the strings are... i just bought the bass. I know I need to change the strings, but i haven't gone to the music store yet... maybe i'll try that.

YEah. Try new strings. Hopefully that'll fix it. I know when my strings are old they can get flakey.

YEah. Try new strings. Hopefully that'll fix it. I know when my strings are old they can get flakey.

Yes Always put on new strings before mucking about with intonation.

So I got new strings, put them on and set the intonation. I'm happy w/ the 1st, 7th and 12th frets but the 5th fret on all 4 strings is still a hair sharp. I don't think it's very noticeable (think about 5 cents) but... is there a specific reason why that would be?

sounds like a bad neck or cruddy fret job

So I got new strings, put them on and set the intonation. I'm happy w/ the 1st, 7th and 12th frets but the 5th fret on all 4 strings is still a hair sharp. I don't think it's very noticeable (think about 5 cents) but... is there a specific reason why that would be?
If you picture the cross section of a fret it is circular or ovular in shape. When the fret is crowned (shaped) the highest point on the fret should be Top Dead Center. If care is not taken, TDC can be anywhere on the fret. When that occurs the intonation will not be true. If the fret is more ovular it is sometimes difficult to achieve this goal. This can also happen through fret wear.

Most people will not hear the difference in pitch when it is off by a couple of cents.