Windhorst's research is in astronomy, cosmology, galaxy formation and evolution, the cosmic dark ages and the epoch of First Light, and astronomical instrumentation. Since the early 1990's, his group at ASU has contributed significantly to unraveling the formation and evolution of distant galaxies with the Hubble Space Telescope, and the role that supermassive black holes and Active Galactic Nuclei have played in the process of galaxy assembly. He is one of the world's six Interdisciplinary Scientists for NASA's 6.5 meter James Webb Space Telescope (JWST) to be launched in 2021. His group at ASU plans to use JWST to map the epoch of First Light in detail.