Apple cider vinegar is simply a vinegar made from apple juice or apple cider. It comes in two versions: filtered and unfiltered. Does it make a difference which one you use? Much depends on what you are doing with it.
ACV Has Mother Issues
Filtered apple cider vinegar is made with apple juice and water. The filtering process removes the vinegar "mother" and any sediment, leaving a clear, amber-colored vinegar. Additionally, it is likely that this vinegar has been pasteurized, which further refines and clarifies it. Unfiltered apple cider vinegar is also made from apple juice and water, but the mother hasn't been filtered out and it likely isn't pasteurized. Its appearance is cloudy and may contain small amounts of sediment.
So the only difference between the two is the "mother," which is simply a somewhat murky collection of cellulose and acetic acid bacteria. It's this mother that transforms alcohol into vinegar (along with the presence of oxygen). What impact does the mother have on the vinegar? Is it important?
When to Use Which
Culinarily speaking, the vinegars are interchangeable — they both have an acedic acid level of 5 percent and a mild sweetness from the apple juice. Often, but not always, the unfiltered version is organic. So if you are interested in less processed, raw, or organic ingredients, or if you want to use ACV to kickstart your own homemade vinegars, then go for the unfiltered kind. I personally find it a touch more apple-y in flavor than the more refined, filtered version — but perhaps that's just me.
While the differences between the two vinegars is simple and straightforward, the feelings around apple cider vinegar's health claims are much more controversial. Many people believe drinking small amounts of unfiltered ACV will lower cholesterol, regulate blood sugars, and prevent heartburn and acid reflux, among other things. And many people think this is a bunch of hooey. (You only have to visit this post from a year ago on ACV and browse through the comments to get a sense of just how controversial these claims are.) Studies have been conducted and it seems like the truth is somewhere in the middle.
So which vinegar should you buy? It depends on what you plan on using it for. Again, the unfiltered version contains a live mother, which you can use to make your own vinegar. It is also less processed and (to my taste) has a little more complexity in flavor. If you're a believer in the health claims or just generally interested in less refined food, then this is the vinegar for you. If you think all that is a bunch of hooey and you want to save a few pennies, then go for the filtered, pasteurized version.