Arthur Clough was born in Liverpool to James Butler Clough, a cotton merchant of Welsh descent, and Anne Perfect, from Pontefract in Yorkshire. James Butler Clough was a younger son of a landed gentry family that had been living at Plas Clough in Denbighshire since 1567. In 1822 the family moved to the United States, and Clough's early childhood was spent mainly in Charleston, South Carolina. In 1828 Clough and his older brother Charles Butler Clough (later head of the Clough family of Llwyn Offa, Flintshire and Boughton House, Chester, a magistrate and Deputy Lieutenant) returned to England to attend school in Chester. Holidays were often spent at Beaumaris. In 1829 Clough began attending Rugby School, then under Thomas Arnold, whose belief in rigorous education and lifestyles he accepted. (See Muscular Christianity.) Cut off to a large degree from his family, he passed a somewhat solitary boyhood, devoted to the school and to early literary efforts in the "Rugby Magazine". In 1836 his parents returned to Liverpool, and in 1837 he won a scholarship to Balliol College, Oxford. Here his contemporaries included Benjamin Jowett, Arthur Penrhyn Stanley, John Campbell Shairp, William George Ward and Frederick Temple. Matthew Arnold, four years his junior, arrived the term after Clough had graduated. Clough and Arnold enjoyed an intense friendship in Oxford.