In 1900, after two years of teaching at Wesleyan University, Woodrow Wilson and family packed their bags and moved to New Jersey, where he accepted a professorship at his alma mater, Princeton University. Although Wilson had been happy in Connecticut, he still felt that he was not achieving his full academic and professional potential, and reasoned that Princeton would provide more opportunities to do so. While at Princeton he wrote and published Division and Reunion in 1893, a work that charted the course of American history from the 1830s to Reconstruction after the Civil War. He also published a biography of George Washington in 1897 and published a large five-volume History of the American People in 1902. In addition to his books, Wilson also authored dozens of magazine articles, editorials, pamphlets, and essays. He intended to write a crowning work that he planned to call The Philosophy of Politics, but was called to other duties before he even began to research the subject.

Just as at Bryn Mawr College and Wesleyan, Wilson was received at Princeton with much enthusiasm; he was lauded as an excellent professor of political economy and jurisprudence who could make his lectures both interesting and informative. He also taught public administration, English law, international law, and constitutional law. Hundreds of students attended his lectures; his popularity was unequaled. His fame as an orator and teacher spread throughout the American academic world. While a professor at Princeton, Wilson was offered the chairmanship of the history departments at the University of Chicago and at Johns Hopkins University (to replace his former professor Dr. Herbert Adams), and he was offered the presidency of numerous other schools, including the University of Illinois and the University of Virginia. Yet he declined to accept any of the offers, preferring to remain at the school he loved. His twelve years as a Princeton professor were among his most challenging and stimulating.

Ever a religious man, Wilson and his wife Ellen joined the Second Presbyterian Church in 1897. That same year, Woodrow also became a governing elder of the church. In 1905, after trying to unite the First and Second Presbyterian Churches into one body, he withdrew his membership from the Second congregation and entered the First as an elder. Throughout this period Wilson retained every ounce of the strict sense of morality that his father and the church had instilled in him during his youth.

Wilson also became a leader among the Princeton faculty members. During his teaching years at Princeton, many both inside and outside the university believed the quality of education had been waning and that Princeton was losing its place among the nation's top schools. Many of the teachers, led by Wilson, cried for higher standards and better leadership to guide the university into the new century. When the university's president, Dr. Francis L. Patton, caved into popular demand and resigned his position, the faculty and trustees of the school looked to Wilson to lead them, unanimously electing him president of the university in 1902. He was the first Princeton president who had not previously been a clergyman.

President Wilson stepped up to the task of strengthening and reorganizing Princeton with vigor, and was blessed for the first five or six years with almost complete support from the faculty, trustees, and even students. Furthermore, for the first time in his career, he was in a position to write policy and to make changes. Wilson began a series of reforms designed to convert the school from a "place where there are youngsters doing tasks to a place where there are men thinking." The reformist attitude and tendencies he developed during these years would stick with him throughout the remainder of his political career.

The first task Wilson set out to accomplish was reorganizing the university budget to fund his visionary reforms. With a check for six million dollars from the trustees, he set about allocating money to various departments, including the undergraduate college, a new school for science, a fund for new teachers and facilities, a new graduate school, a school of jurisprudence, a natural history museum, and a school for electrical engineering. He then set about redesigning the methods of teaching undergraduates, transforming the system to a style modeled after a program used at Oxford University. Entitled the preceptorial system, this method of teaching brought small groups of students together under the tutelage of a professor trained in their chosen field rather than in large impersonal lecture halls. The system was devised to stimulate thinking, student-teacher interaction, and discussion rather than requiring students to memorize information. Nothing like the preceptorial system existed anywhere else in the United States at the time, and it quickly helped push Princeton back up into the ranks of elite American universities. Many modern universities and colleges throughout the country now have similar programs based on Wilson's revolutionary method.

President Wilson also reorganized the undergraduate program's degree requirements. At the time, many colleges and universities, including Princeton, used the free elective system to allow students to select a course of study during their four years without having to meet any standard requirements. This system let many students graduate from the university with specialized knowledge in a single field and little knowledge of anything else. Struck by the lack of well-roundedness in the school's graduates, Wilson and the faculty altered the program, requiring all undergraduates to pass certain courses from a variety of fields during their four years in order to graduate. Furthermore, to increase the quality of students at the university, Wilson drastically increased the entrance requirements. This raised a row among wealthy individuals accustomed to buying their sons' education, but Wilson and the trustees held their ground.

While attempting to improve the quality of education via requirement changes and teaching methods, Wilson also initiated reform to raise standards by attacking the university's social circles that fostered elitism and snobbery. Although the university had always banned Greek organizations, other cliques evolved over time in the form of "eating clubs." During his undergraduate years, Wilson himself had been a member of the Alligators, and other organizations like it lined both sides of Prospect Avenue near the college. Again with the support of the trustees, and even with the support of many of the students and members of the eating clubs, Wilson attempted to revise the system and initiate his quadrangle plan. Also similar to the Oxford system, the quadrangle plan called for housing undergraduates in separate semi-autonomous buildings or colleges throughout the campus. Each college would surround a central courtyard and serve as a dormitory, dining facility, and place where students could receive individual tutoring and instruction in their fields. Each college was also intended to house a variety of students with different plans of study to increase diversity.

This plan was revolutionary at the time, and met much more opposition than the preceptorial system. Many of the university's alumni fought against the idea, claiming that the quadrangle plan would destroy all the camaraderie and spirit that the eating clubs fostered. A battle over the subject ensued for several years until the trustees finally withdrew their support of the quadrangle plan. Without any support, Wilson was forced to abandon the idea, and the eating clubs remained. However, years later, systems similar to the quadrangle plan were initiated at schools around the country, including Princeton's rivals Harvard and Yale.

Near the end of his presidency at Princeton, Wilson fought additional battles, the most destructive of which occurred over his plans for a new graduate school building. Wilson wanted the new building to be constructed in the center of the undergraduate campus to promote the exchange of ideas between undergraduate and graduate students. Dean Andrew Fleming West opposed the idea. He envisioned a graduate school that was separate from the college to promote higher learning that was beyond undergraduate studies. The two men tenaciously held onto their ideals and fought each other for several years. The controversy divided the trustees and faculty into two distinct factions. Wilson succeeded in building a coalition of trustees and alumni powerful enough to support his plan, but when a former alumnus unexpectedly died and willed several million dollars to the University on the condition that the new graduate school be built according to West's plan, Wilson conceded. Ironically, it was later determined that the willed estate did not amount to the several million dollars as originally believed, but only $600,000.

The eight years Wilson served as president of Princeton were particularly tiring years for him. While he made sweeping reforms through the school and education system, he continued to teach and lecture as he had done before. He did most of this himself with only the assistance of a part-time secretary. The work took a heavy toll on him: throughout his service he had several borderline nervous breakdowns, and in May of 1906 fell from a stroke caused by arteriosclerosis that left him temporarily blind in his left eye. His physicians urged him to quit, but he refused and instead chose to vacation with his family in Great Britain that summer.

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