If you have a high risk for heart attacks, or a strong history of heart disease or diabetes, drinking too much unfiltered coffee could have a negative affect on your health. Unfiltered coffee may raise blood cholesterol levels of homocysteine, an amino acid found in our bodies. Texas Tech Medical Center's Dr. Gary Meyerrose says elevated homocysteine may be caused by diterpenes which are chemicals found in coffee and are known to increase cholesterol levels. So it's both the fats that cause the cholesterol to go up and also maybe this tendency for a little bit of rise in homocysteine. Studies conducted in the Netherlands show running coffee through a filter can trap harmful oils and fat.
Filters can also counteract a rise in homocysteine.
So like I said, it seems to me even though it's a small risk factor compared to other things we have in our lives, it's a small thing to use a filter instead of not to use a filter.