Dorothy Hodgkin's mentor Professor John Desmond Bernal greatly influenced her life: scientifically, politically, and personally. 

Bernal was a key scientific adviser to the UK government during the Second World War. He was also an open and vocal member of the Communist Party and a faithful supporter of the Soviet regime until its invasion of Hungary in 1956. Hodgkin always referred to him as "Sage"; they were lovers before she met Thomas Hodgkin. The marriages of both Dorothy and Bernal were unconventional by the standards of the present and of those days.

In 1934, at the age of 24, Dorothy began experiencing pain in her hands:a visit to a doctor led to a diagnosis of rheumatoid arthritis which would become progressively worse and crippling over time, with deformities in both her hands and feet. In her last years, Hodgkin spent a great deal of time in a wheelchair but remained scientifically active despite her disability.

In 1937, Dorothy Crowfoot married Thomas Lionel Hodgkin. He had not long returned from Palestine where he had resigned from the Colonial Office and was working in adult education. He was an intermittent member of the Communist Party and later wrote several major works on African politics and history, becoming a well-known lecturer at Balliol College in Oxford.The couple had three children: Luke (b. 1938), Elizabeth (b. 1941) and Toby (b. 1946).