There is a difference over time, but that doesn't kick in until the cotton fibers start to break down at around 20 years. For the first 15 years, other than possibly a difference in the rate the color fades, it won't make any difference. After that, the poly fibers, which are stronger, will rub/pull on the cotton fibers and cause them to break more quickly than if it were all cotton. The other issue is that poly thread fades much slower than cotton so after a good number of years, threads that started the same color will be 2 different shades of that color.