We aren’t totally sure. We have a lot of clues, but no smoking gun. There are detectable genetic differences, which seem to correlate to measurable differences in brain anatomy and function. There’s been some work done suggesting that people who stutter monitor their own speech differently than people who do not. Nobody is sure which of these are cause and which are effect (though I’d wager the genetics are definitely part of the cause, even if we aren’t sure how yet).