In 1995 he was appointed an assistant professor of medicine at the Harvard Medical School and as associate physician at the Brigham & Women's Hospital, and in 1996 as Field Marshal Alexander Professor of Cardiovascular Medicine in the University of Oxford.

[1][2] Watkins was elected to Membership of the Royal College of Physicians (MRCP) in 1987, graduated MD and PhD from the University of London in 1995, and was appointed a Fellow of the Royal College of Physicians (FRCP) in 1997.

[1] At Oxford, Watkins is the Director of the British Heart Foundation's Molecular Cardiology Laboratory in the Wellcome Trust Centre for Human Genetics and of its Centre of Research Excellence, one of six similar programmes in the United Kingdom.

[3] Watkins's main specialism is in molecular genetic analysis of cardiovascular disease, and his most notable work is on the inheritance of heart disease, especially on hypertrophic cardiomyopathy and the genetic causes of "sudden cardiac death".

He is chairman of an international group which investigates genetic susceptibility to coronary artery disease, which has funding from the European Commission.