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Background  The rural family physician program and social protection scheme were started in Iran about 10 years ago, and no comprehensive study has been carried out to investigate the effects of this program on mortality-related health indicators yet. The present study aims to examine the impacts of implementation of the family physician program and rural insurance program, which was launched in June 2005, on neonatal (NMR), infant (IMR), and under-5-year (U5MR) mortality rates in rural areas of Iran between 1995 and 2011, using a time-series analysis.    Methods  Three segmented regression models were built to evaluate the effects of the program on NMR, IMR, and U5MR, and several independent variables were entered into the models, including annual incremental effect of the program (variable of interest), time effect, behvarz density, effect of the family physician and rural insurance programs, as well as socioeconomic variables including years of schooling, wealth index, sex ratio, and logarithmic scales of rural population size in each area. Data were gathered from secondary sources and other studies. Data pertaining to the year 2007 were excluded from the final analysis due to their inaccuracy.    Results  Our results show that the incremental effect of implementing the rural family physician program is associated with significant reductions in NMR ( β  = − 0.341.  p  −  value  = 0.003) and IMR ( β  = − 0.016.  p  −  value  = 0.009). Although the association between this effect and reductions in U5MR were evident, they were not statistically significant ( β  = − 0.003.  p  −  value  = 0.542). Moreover, wealth status of inhabitants was associated with reductions in NMR ( β  = − 0.889.  p  −  value  = 0.001), IMR ( β  = − 0.052.  p  −  value  < 0.001), and U5MR ( β  = − 0.055.  p  −  value  < 0.001) in the time period of the study.    Conclusions  In this nationally representative study, we showed that implementation of the second health system reform in Iran, known as the family physician program and social protection scheme for rural inhabitants, is associated with significant reductions in NMR and IMR. However, reported reductions in U5MR were not found to be statistically associated with the launch of the program.  The advantage of this study was the ability to depict a more precise picture of the outcomes of a national-level intervention.    Electronic supplementary material  The online version of this article (doi:10.1186/s12963-017-0138-0) contains supplementary material, which is available to authorized users.

Impact of rural family physician program on child mortality rates in Iran: a time-series study