Last week, C. Clairborne Ray of the New York Times answered this question as part of the paper’s Q&A feature: bookofjoe: What makes coffee bitter?. (I’m citing it on another blogger’s post instead of the original NY Times source — in case you are religiously opposed to NYT logins.)

As the article states, coffee is a “complex chemical soup”. So complex, in fact, that the answer they offer is a complex alphabet soup.

The digestible short of it is that a little bitterness isn’t necessarily a bad thing for the overall balance of coffee, as it cuts down on its acidity. However, you can cut back on the perceived bitterness of the cup by avoiding distilled water, by brewing at higher temperatures, and laying off the robusta. The Coffee Research Institute also recommends medium roasts, drip-brewed systems, and using a coarser grind.

NYC coffee needs to spend plenty of time in therapy

UPDATE: Aug. 21, 2007
It’s amazing what old stories get rehashed over and over again. Chemist Thomas Hofman presented findings today at a meeting of the American Chemical Society in Boston, seemingly unaware of the fact that others have bothered to ask the very same question before, leading to prior research reported several times over already: Chemists Find What Makes Coffee Bitter | LiveScience (also: How long before the next scientist reports on gravity research made by dropping objects from the Leaning Tower of Pisa?