Sir Michael succeeds Professor Averil Mansfield, who steps down after completing her one-year term as BMA president.
'The theme I have chosen for my year as president is health inequalities and I hope to assist the BMA with its work in this area,' he said.
'Doctors are in a unique position to speak out for their patients and to call for more resources to be spent on preventing disease.'
Sir Michael is a world expert in health inequalities and the social determinants of health and has led a research group on this issue for the past 30 years.
He chaired the WHO Commission which produced its report in 2008 entitled 'Closing the gap in a generation: health equity through action on social determinants of health'.
He is also the director of the International Institute for Society and Health and a Medical Research Council research professor of epidemiology and public health at University College London.
In 2000, Sir Michael was knighted for services to epidemiology and understanding health inequalities.
Prof Mansfield will be remaining with the BMA as she takes over as chairman of the Board of Science.