The cores of compact stars reach the highest densities in nature and therefore could consist of novel phases of matter. We demonstrate via a detailed analysis of pulsar evolution that precise pulsar timing data can constrain the star’s composition, through unstable global oscillations (r modes) whose damping is determined by microscopic properties of the interior. If not efficiently damped, these modes emit gravitational waves that quickly spin down a millisecond pulsar. As a first application of this general method, we find that ungapped interacting quark matter is consistent with both the observed radio and x-ray data, whereas for ordinary nuclear matter some additional enhanced damping mechanism is required.