The research, which will be reported to next week's meeting of the region's education committee, was carried out by Edinburgh University's Centre for Educational Sociology.
The findings challenge the picture of secondary school performance given in the Government's tables of exam statistics, and show that only two Grampian secondaries did not share in the region's general rise in pupil attainment as measured by the value added to pupils' progress. But the report notes that significant differences between schools remain and states that "there is no room for complacency".
Family backgrounds and neighbourhoods make the most profound impact on examination performance. A difference of five-and-a-half Standard grades in the"raw" averages between the Grampiansecondaries with the best and worstresults was reduced to just one Standard grade after taking account of varying pupil intakes.
The study also focused on the significance of what it calls "school social context", the effect that family background of the school population as a whole has on individual pupils. The researchers concluded that "the attainment of an 'average' pupil may be raised or lowered by two or three Standard grades by differences in school social context".
As a result, there are "serious inequalities in pupils' examination results". The research suggests pupils from disadvantaged backgrounds would have better grades if they attended schools with a large number of pupils from better-off families.
The report, produced at a cost of Pounds 241,000, acknowledges that information on pupil performance in primary schools would allow a more accurate measure of how well schools do in taking their pupils from S1 to SCE examinations.
The researchers also investigated pupils' experience of schools. They found that more than three-quarters of pupils agreed with statements that "school work was worth doing", "discipline was fair", and "my teachers helped me to do my best".