He had a reputation as something of a workaholic, though a stroke in 1896 compelled him to reduce his active business involvement. His eldest son William Henry Vanderbilt II (1870-1892) had died while a junior at Yale University, and Cornelius endowed a large dormitory there. He disinherited his second son Cornelius Vanderbilt III (1873-1942) for marrying without his permission. Third son Alfred Gwynne Vanderbilt Sr (1877-1915) went down with the RMS Lusitania. His remaining son was Reginald Claypoole Vanderbilt. His daughters were Gertrude Vanderbilt Whitney and Countess Gladys Szechenyi.
The fabulous Fifth Avenue mansions he, his brothers, and his sons lived in have been demolished, but the Newport, Rhode Island vacation home he built, The Breakers, still stands as a memory of the lifestyle of Cornelius Vanderbilt II.
On his death, family leadership passed to his brother, William Kissam Vanderbilt. His philanthropy had been such that he did not increase the wealth that had been left to him.