Fischer had a complex relationship with his single mother, Regina. While she supported his chess ambitions, their relationship was often strained. She had strong political views and was very active politically, which sometimes caused friction.

Fischer's biological father was Hans-Gerhardt Fischer, a German biophysicist. He never knew his biological father. His mother's ex-husband, Paul Nemenyi, may have been his real father, but this was never conclusively proven. The absence of a consistent father figure likely impacted his development.

Fischer's intense focus on chess left him with limited time for social relationships. He had few close friends and rarely engaged in traditional social activities.

In his later years, Fischer claimed to have secretly married Miyoko Watai, the President of the Japanese Chess Association. Her claim to Fischer's estate was contested, but ultimately upheld by Icelandic courts.

In his later years, Fischer became increasingly isolated and paranoid. He expressed conspiracy theories and made controversial statements, further alienating him from the mainstream.