He appears to have gone beyond his own advice, since though he and his wife were married for over 40 years, they never had sexual intercourse and had separate bedrooms all their lives.

Kellogg was also outspoken on his beliefs on race and segregation. In 1906, Kellogg founded—together with Irving Fisher and Charles Davenport—the Race Betterment Foundation, which became a major center of the new eugenics movement in America. Kellogg was in favor of racial segregation and believed that immigrants and non-whites would damage the gene pool.