Carroll is at the forefront of a field known as evolutionary developmental biology ("evo-devo"). He is also the author of Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom (ISBN 0-393-06016-0), one of the first popular summary narratives of the field. He is a professor of genetics, medical genetics, and molecular biology at the University of Wisconsin—Madsion, and an investigator for the Howard Hughes Medical Institute. Additionally, he writes a monthly column for the New York Times called "Remarkable Creatures." He is a strong advocate of the primacy of cis-regulatory evolution in the context of morphological evolution.

He is also the author of The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution (ISBN 0-393-06163-9), in which he argues for the irrefutable existence of natural selection by detailing numerous examples of DNA which has recently been traced from current species to long extinct ones.

Carroll received his bachelors at Washington University. He then received his Ph.D. in immunology from Tufts University.