I am not a quilt store owner but I will pass along what I have been told. The difference is if you buy fabric from a quilt store, they receive the first run of the fabric. As fabric is woven the weave becomes looser at the ends. So, when a quilt shop orders their fabric, generally they receive their portion from the best part of the run; that being the best and tightest weave. When they get to the portion where the weave is not as tight (good) then those portions are bought by Joann's, etc. I can only tell you that you have to feel the fabric and see it to know if it is first quality. I buy from all over- quilt shops, Joann's, and even on line. If I am doing something special, I head to my quilt shops. If I am doing a charity quilt, I buy the best for the money I have available. Hope some of this helps.