The move comes after a report by Chief Medical Officer Harry Burns warned "magic bullet" policies such as the smoking ban and healthy eating drives had actually increased health inequality as affluent people were more likely to respond.
Head of the Public Health Observatory Dr Gerry McCartney welcomed the move, but said the Scottish Government would be "climbing a hill" in the face of UK welfare reforms.
He said: "We do well in almost every other measure – on education, on economic growth, in academia. But the one thing we compare really badly on – and we compare badly against every other country in Western Central Europe – is on our health record.
"What Michael Matheson is saying about tackling the social and economic inequalities in Scotland – that'll generate benefits for average health, it'll narrow health inequalities, but it'll also start to impact on educational inequalities and reduce crime, because we know from research more equal societies do well on a whole range of factors."