I suppose it's an individual choice, like most everything in quilting. Personally, I'm quite happy to be a 'natural' fabric snob, i.e., those made from plant or animal fibers. I just can't imagine making quilts out of petroleum byproducts. Polyester doesn't breathe, it melts and sticks to the skin when ignited, it's non-biodegradable, and I just choose to avoid using it in anything that goes into my quilts - fabric, batting and thread included.
