Beginning at age 16 in the Preparatory Department, Morgan attended the State College of Kentucky (now the University of Kentucky). He focused on science; he particularly enjoyed natural history, and worked with the U.S. Geological Survey in his summers. He graduated as valedictorian in 1886 with a Bachelor of Science degree. Following a summer at the Marine Biology School in Annisquam, Massachusetts, Morgan began graduate studies in zoology at the recently founded Johns Hopkins University, the first research-oriented American university. After two years of experimental work with morphologist William Keith Brooks and writing several publications, Morgan was eligible to receive a master of science from the State College of Kentucky in 1888. The college required two years of study at another institution and an examination by the college faculty. The college offered Morgan a full professorship; however, he chose to stay at Johns Hopkins and was awarded a relatively large fellowship to help him fund his studies.