He was the grandson of Alfred Cowles, Sr., who was a founder of the Chicago Tribune. His father, Alfred Cowles, Jr. (1865–1939) managed and directed the Chicago Tribune from 1898 to 1901 and the American Radiator Company. His mother was Elizabeth Cheney (1865–1898). His parents lived at 1130 N. Lake Shore Drive in Chicago, Illinois. Alfred Cowles III had three siblings: Knight Cheney Cowles (born 1892); John Cheney Cowles (born 1894); and Thomas Hooker Cowles (born June 6, 1895) who married Barbara Granger, daughter of architect Alfred Hoyt Granger.
^"YALE 'TAPS' IN RAIN AMID GREAT TENSION: Nervousness of the Marshaled Juniors Reflects Owen Johnson's Attack on the System. YALE GRIT PUTS IT THROUGH Recent Graduate Predicts Change Soon -- Harriman and Cortelyou Get Bones, Webb and Camp Keys.". New York Times. 17 May 1912. p. 8.|accessdate= requires |url= (help)
^The Cheney Genealogy by Charles Henry Pope, published by Richardson Reprints, 1897. p. 487
^The Book of Chicagoans, published by A.N. Marquis, Chicago, IL, 1911