On June 1, 1887 in St. Paul, Minnesota, Warren married Lilian Baker (born November 19, 1862 in Cambridge, Ohio). Their only son, Lewis Baker Warren was born in St. Paul on November 23, 1888. Lewis matriculated at Yale University and was injured in a football game, playing without a helmet.Rock Island (Ill.) Argus, September 29, 1908, p. 4 He died in Manhattan on November 5, 1912. Charles Warren endowed a scholarship at Yale in memory of Lewis in 1914; this was augmented by a $1,000,000 bequest from Charles's estate in 1936 after his passing.Lawrence A. Martin, ed., Railroads in Minnesota, Part II, April 28, 2010
