Professor Huterer's principal interest is in understanding the nature and origin of "dark energy", a mysterious component that dominates the dynamics of the universe and causes its accelerated expansion. The physical mechanism behind dark energy is one of the great unsolved mysteries of modern physics and astronomy. Professor Huterer uses cosmological probes to study the effects of dark energy on the structure in the universe, and their data in turn inform our fundamental understanding of what powers the accelerated expansion. These probes include measurements of distances to type Ia supernovae, mapping the growth and evolution of the large-scale structure in the universe, and gravitational lensing. Professor Huterer is currently actively involved in analyzing and interpreting data from the Dark Energy Survey, currently the world's most powerful survey of the large-scale structure in which Michigan cosmologists play a major role. In 2017, Professor Huterer was appointed a coordinator of the Theory and Combined Probes working group within the DES.

Professor Huterer is also actively involved in studying the isotropy of the universe and the distribution of primordial inhomogeneities that seeded structures observed on the sky today. In 2008, he and his collaborators discovered a novel signature of departures from Gaussianity in the initial distribution of matter in the universe that can be observed in the spatial distribution of galaxies in current and future surveys. This finding energized research of the tests of primordial physics, as it enabled many times more precise measurements of the early universe physics with galaxies than previously thought possible. Professor Huterer also studies the structure of the universe on the largest spatial scales using a combination of cosmic-microwave-background and galaxy-distribution maps of the universe.