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Before attending Harvard University in 1676, he attended the Boston Latin School. This school was open to all boys regardless of class, and served to educate and prepare the young men for university. The Boston Latin School is where Brattle met influential Puritan leader Cotton Mather. Although the two men agreed on many social and political ideologies later in life, they did not see eye to eye during their time at the Boston Latin School. It is documented that Thomas Brattle and other schoolmates enjoyed picking on Cotton Mather (to the point where he wrote to his father, Increase Mather, and requested to come home early). After his time at the Boston Latin School, Brattle attended Harvard University and received an AB in mathematics and science.