As you can see they are both composed of long glucose chains and have a fairly similar structure, although the amylopectin is highly-branched. I have been looking through the literature to see if there is any meaningful difference between the two in terms of health benefits. The evidence is mixed, but it seems that amylose is considered by more researchers to confer health benefits over amylopectin because it is more slowly digested, thus giving amylose a lower glycemic index. Again, the evidence is not so clear-cut so avoiding amylopectin like the plague is probably unnecessary.