How to Set Guitar Intonation

Why your guitar is in tune open but sour at the 12th fret — and the fix.

Intonation is whether your guitar plays in tune at every fret, not just on the open strings. A perfectly tuned open string can still read sharp or flat at the 12th fret if the saddle position is wrong. If your chords sound great in first position and increasingly off as you move up the neck, this is your problem.

Do this last

Intonation depends on both neck relief and action height — both change the string's effective vibrating length. Set those first (see the setup order), or you'll be setting intonation twice.

The method, string by string

Tune the open string dead-on. Use a tuner, not your ears — you're working within a couple of cents.
Fret the 12th fret and check the tuner. Play the fretted note (not the harmonic) with your normal playing pressure — pressing hard pushes it sharp and lies to you.
Compare. The fretted 12th-fret note should match the open string within ±2 cents.

Adjust the saddle:

12th fret reads…	Move the saddle	Why
Sharp	Back (away from the neck)	Lengthens the string, flattens the pitch
Flat	Forward (toward the neck)	Shortens the string, raises the pitch

Retune the open string — moving the saddle detunes it — then check the 12th fret again. Repeat until it matches.
Work through all six strings, low E to high E. On a Strat the adjustment screws are at the back of the bridge plate (Phillips head); on a Tune-o-matic they're at the front or back edge of the bridge.

Why intonation goes off at all

Pressing a string to a fret doesn't just shorten it — it stretches it slightly, which raises the tension and pushes the note sharp. Fret positions are calculated for an ideal string with no stiffness and no height above the fretboard; real strings have both. The saddle compensates by making the string slightly longer than the theoretical scale length.

Different strings need different compensation: wound strings (E, A, D) are stiffer and need the saddle further back; plain strings need less. That's why a properly intonated bridge has that characteristic staggered saddle pattern — low E furthest back, high E closest to the neck. It's also why changing string gauge (or even brand) shifts intonation: check it after every string change.

When one string won't intonate

If the 12th fret is still sharp or flat with the saddle at the end of its travel, something else is wrong. In order of likelihood:

A dodgy string — kinked or badly wound. Swap it first; it's the cheapest fix.
A worn fret, especially at the 12th — the contact point moves off the fret's crown.
A badly cut nut slot pulling low-position notes sharp.
Persistent problems on multiple strings can indicate a neck or bridge positioning issue — that one's a tech visit.

Or let GuitarDoc guide you

GuitarDoc Pro's guided intonation mode walks you through every string — open, 12th fret harmonic, fretted note — then tells you which way to move the saddle and how far off you are, down to the cent. The strobe tuner itself is free forever. One-time purchase. Offline. No subscription.

Coming soon to the App Store

More guides: Setup order · Truss rod & neck relief · Action height · Fix fret buzz