I'm a newbie player and unfamiliar with intonation. My acoustic sounds great, but it is not intonated at all.

I'm thinking that intonation for an acoustic is more complex than an electric. Got a new set of strings for my stratocaster and intonated no problem. Do you need to actually make 'physical' changes to an acoustic's structure - it seems that way to me.

Many thanks.
Intonation on acoustic guitars is always off. If the guitar's intonation is properly set when it leaves the factory (and they are) then by the time you actually get around to buying the guitar from the music shop, the intonation is already 20 cents sharp on the 12th fret. Sometimes this can be fixed again later on by simply reshaping the saddle but unfortunately only 1/8" saddle actually supply you with enough material to reshape them. Most modern guitars use much narrower saddles that don't allow for intonation adjustments.

The good news is that an acoustic guitar is always blending several notes together into 1 dominant tone. The top of the guitar gives you 3 or 4 tones, the back gives you just as many, the guitar's air chamber has it's own resonate frequency, the sides even produce sound. When you mix all this with the sound generated by the string you are actually looking at hundreds if not thousands of different sounds all being generated at once. If the string is sharp by 20 or 30 cents on the 12th fret chances are you won't notice because there are so many other sounds in the mix.

Electric guitar doesn't have this luxury. There are far fewer overtones and a lot more tone coming from the string it's self so when an electric string is 20 cents sharp on the 12th fret every chord sounds wrong.

So to sum it up, don't worry about acoustic intonation unless you are having noticeable issues with tuning. If there are tuning issues try and work around them if you can. If you can hear that the G string is sharp on fretted notes the try tuning it 10 cents flat when open and hopefully the sharp and flat will balance out. If you do need to make adjustments you have to do so by filling away part of the saddle. If the saddle is too narrow and won't give you the range you need then the guitar will have to be taken to a luthier, routed for a larger saddle, and then intonated.
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I wonder if people who talk about intonation here are often actually understanding what it means?

Most all modern guitars are produced with very accurate fret placement and saddle placement. It's rather unusual for even very inexpensive acoustic guitars to be "out" to any noticeable degree.
Better guitars are checked more carefully, of course, and are often delivered with a compensated saddle to get things spot-on.
What usually is going on is not that the intonation is bad, but that the action is too high. Often guitars are delivered with the action deliberately on the high side, since manufacturers know that picky guitarists will want it adjusted to their personal tastes.
It's much easier to lower the action than to raise it... So they make it on the high side.

The beginner often doesn't know this, so they suffer with fingers that are more sore than need be and also find that as they fret notes on the upper frets, they sound "out".
This because you are "pulling the string sharp" by the excessive travel to the fret. An action adjustment usually corrects the problem.

If, for some reason, the intonation is actually bad, if the saddle was improperly installed or the fret-spacing machine was malfunctioning or whatever... Then that would be a warranty problem.

For an older instrument... Difficult. Often the saddle has to be removed, the slot filled, a new slot routed... Big job. In some extreme cases, two saddles, a "split" saddle, can be used.
Many thanks for replying with a really comprehensive explanation. Good of you to take the time.
Many thanks for replying with a really comprehensive explanation. Good of you to take the time. Off topic: I passed through Newtown on my way back up north from Cardigan - it's a journey I have done many times. Small world, eh.