Family
- grandmother : Cherokee
- father Eugene Kilmer: born in 1921; made and lost a fortune developing real estate on a ranch once owned by Roy Rogers; divorced from Kilmer's mother c. 1968; died in April 1993
- mother Gladys Kilmer: divorced from Kilmer's father c. 1968
- cousin Joyce Kilmer: second cousin twice removed; best-known for the poem "Trees"
- brother Mark Kilmer: born on March 19, 1958; estranged from Kilmer since their father's funeral
- brother Wesley T Kilmer: born on May 13, 1961; drowned in September 1977 during an epileptic fit in the family swimming pool when he was 16
- daughter Mercedes Kilmer: born on October 29, 1991 in Santa Fe, New Mexico; mother, Joanne Whalley
- son Jack Kilmer: born in June 1995; mother, Joanne Whalley
Companions
- Cindy Crawford: dated in 1996
- Daryl Hannah: began dating in 2001
- Drew Barrymore: reportedly dated c. 1995
- Ellen Barkin: dated c. 1984
- Jaycee Gossett: dated from late 1998 to c. 2000
- Mare Winningham: had a three-year relationship during high school
- Michelle Pfeiffer: wrote poetry for her, remembering her in his book of poetry, "My Eden After Burns"
- Cher: dated briefly in the 1980s
