Soon tired with the practice of law, Wilson decided that the second best way to become a great statesman and policy maker was to further his education. Within two days of becoming engaged to Miss Ellen Axson in 1883, young Woodrow headed off to Johns Hopkins University. The school was small compared to other older American universities, but many of the nation's best and brightest flocked to its campus in Baltimore. Wilson himself had heard of the school through close friends, and had decided to apply to receive some postgraduate training.

Although the University had just recently been founded, it was already stirring up a whirlwind in the academic world for its unprecedented rigor and intensity. Ironically, however, even though Hopkins was known for its difficulty, its professors discouraged their students from taking courses merely to attain a Ph.D.–which in their opinion meant only that a student had met the necessary requirements but had not necessarily been educated. Because of this, many of the students, including Wilson attended, the school not to receive any specific advanced degrees, but to receive an education. Indeed, it was not until nearly the end of his stay at Johns Hopkins that Wilson decided to pursue a doctorate.

Wilson found that the academic challenge at Hopkins lived up to its reputation, and he studied as he never had before. His studies included American history, international law, political economy, jurisprudence, constitutional history, and German. His most difficult course by far was his "Historical Seminary" taught by the well known Dr. Herbert Adams, famous for his German methods of teaching and making his students think, infamous for his demand for perfection from his pupils. Although Wilson would later recall that Adams's teaching methods were beneficial in the long run, he hated Adams and the course at the time. Yet, unlike many students, Wilson worked harder because of his hatred for the course and its professor, and soon earned Adams's respect.

Wilson also earned the respect of many others, both within the Johns Hopkins faculty and without. In addition to his regular coursework, he worked on a study that would eventually become his doctoral dissertation. Entitled Congressional Government, the work was an evaluation and analysis of the American legislative branch and system. When published in January 1885, Congressional Government received instant praise from academics throughout the U.S. and Europe as being an unparalleled study of American government. The book also established Wilson as one of the premier American political scientists of the time–an honor few academics can claim at the age of twenty-eight. Moreover, U.S. Navy admiral was so impressed with the book that he ordered a copy of it to be placed on every ship in the Navy. Wilson also collaborated on a study of American economic history with a fellow student; although the book was never published, his research on the subject helped him make more informed decisions as a statesman. Wilson ultimately received his doctorate from Johns Hopkins in 1886.

On June 24, 1885, Wilson married his fiancée, Ellen. The two were married in Savannah, Georgia, by Wilson's father and by Ellen's grandfather, who was also a Presbyterian minister. Afterwards, they honeymooned briefly in a cottage in the woods in North Carolina, and then finally settled in Bryn Mawr, Pennsylvania, where Woodrow had just accepted the post as the first professor of history at the newly-founded Bryn Mawr College for women. Founded by the Society of Friends, the school was modeled after Johns Hopkins and designed to provide young women with the best education possible. The school's first dean, M. Carey Thomas, was later known as one of America's pioneering female educators.

When Wilson first arrived at Bryn Mawr, the school was still very small and lacked the resources of other colleges. The school boasted of only forty-two students, two classroom buildings, and three small houses for the faculty. Wilson's salary was only $1,500 per year. Initially, Wilson was excited at the prospect of teaching at the school. Although the salary was low, the job still provided an income on which he and Ellen could live. Teaching proved interesting at first, and Wilson relished in the fact that he had time to study on his own. While at Bryn Mawr, he began working on The State, the first textbook on comparative government–one that would eventually be regarded as one of the finest examples of Wilson's scholastic abilities, if not his best work.

Within several years, however, Wilson grew tired of the small school, as he saw his colleagues as intelligent but not driven enough. He argued with Dean Thomas over numerous subjects. Most important, Wilson disliked teaching women. Although he was not anti-feminist in the political or social sense–indeed, he would later support the causes of women's rights as President–and even though he considered his wife to be among the best conversationalists and most intelligent human beings he knew, he nevertheless found his female students to be "too literal and unimaginative." He quickly grew tired of teaching them, and desired a classroom of male students. Because of these frustrations, he left Bryn Mawr after three years to take up a teaching position at Wesleyan University in Middletown, Connecticut, in 1888.

Wesleyan proved to be a much more stimulating environment for Wilson. He organized the Wesleyan House of Commons, a debating society for students, and he quickly became known as one of the school's best teachers and lecturers. At this time he also began guest lecturing at Johns Hopkins and continued to do so until 1902. Wilson even began coaching the university football team; he took the collection of untrained players and transformed them into a championship team in just two years. He continued working on The State, which he published in 1898. He also had more time for family: by the end of his term at Wesleyan, Wilson was the proud father of three daughters, Margaret born in 1886, Jessie Woodrow born in 1887 and named for his mother, and Eleanor Randolph born in 1889.

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