There are three possible differences (or lack thereof):

(1) There's no difference at all.

(2) Cider, often times, is not pasteurized. Consequently, it ferments over time, giving it a mildly alcoholic kick. Store-bought apple juice, in contrast, is pasteurized soon after crushing, preventing fermentation and resulting in a pleasant but kickless taste. Does the cider bottle say if it's pasteurized?

(3) Cider is made from apples that are picked early. (Source: Washington State outfit that claims to be the country's largest maker of juice and cider.) Early-harvest apples supposedly have higher acid and lower sugar content, producing a drink with a tangier taste. Thus true cider remains cider after processing because pasteurization doesn't affect the acid/sugar content.

So there you go..it could be something, or it could be absolutely nothing other than a gimmick to make the 'cider' seem more homemade or authentic. Isn't marketing grand?
Source(s):
http://www.straightdope.com/columns/read/391/whats-the-difference-between-a...

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