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Background  In Brazil, 72% of all deaths in 2007 were attributable to non-communicable diseases (NCD). We used a risk and related factor based index to prioritize NCD prevention programs in the combined 26 capital cities and the federal district (i.e., Brasilia) of Brazil.    Methods  We used 2006–2011 data (adults) from census and Brazil's surveillance of 12 NCD risk factors and 74 disease group mortality. The risk and related factors were: smoking, physical inactivity, overweight-obesity, low fruits and vegetables intake, binge drinking, insufficient Pap smear screening (women aged 25 to 59 years), insufficient mammography screening (women aged 50 to 69 years), insufficient blood pressure screening, insufficient blood glucose screening, diagnosis of hypercholesterolemia, diagnosis of hypertension and diagnosis of diabetes. We generated six indicators: intervention reduction of the risk factor prevalence, intervention cost per person, prevalence of risk factor, deaths attributable to risk factor, risk factor prevalence trend and ratio of risk factor prevalence between people with and without a high school education. We transformed risk and related factor indicators into priority scores to compute a priority health index (PHI). We implemented sensitivity analysis of PHI by computing it with slightly altered formulas and altering values of indicators under the assumption of bias in their estimation. We ranked risk factors based on PHI values.    Results  We found one intermediate (i.e., overweight-obesity) and six top risk and related factors priorities for NCD prevention in Brazil's large urban areas: diagnosed hypertension, physical inactivity, blood pressure screening, diagnosed hypercholesterolemia, smoking and binge drinking.    Conclusion  Brazil has already prioritized the six top priorities (i.e., hypertension, physical inactivity, blood pressure screening, hypercholesterolemia, smoking and binge drinking) and one intermediate priority (i.e., overweight-obesity) for NCD prevention identified in this report. Because effective interventions to reduce disease burden associated with each of the six priority risk factors are available, strategies based on these interventions need to be sustained in order to reduce NCD burden in Brazil. PHI can be used to track NCD prevention and health promotion actions at the local and national level in Brazil and in countries with similar public health surveillance systems.    Electronic supplementary material  The online version of this article (doi:10.1186/s12889-015-1787-1) contains supplementary material, which is available to authorized users.

A priority health index identifies the top six priority risk and related factors for non-communicable diseases in Brazilian cities