Purpose We performed this study to assess the trend of geographical disparities between rural areas located in the catchment areas of 41 medical universities in Iran from 1993 to 2008. We evaluated four indicators including rates for neonatal mortality (NMR), infant mortality (IMR), under-5 mortality (U5MR) and crude death (CDR).

Methods We got about 656 university-year data points for each of the indicators (missing data <0.5%). The people under assessment were between 16.7 (in 1993) to 20.1 million (in 2008). We measured disparities through the calculation of index of disparities (ID_isp) and assessed the trends using the Cuzick non-parametric test for trend.

Findings Except for the increasing trend of CDR (Z=+2.83, p=0.005), the others had decreasing trends: NMR (Z=−3.23, p=0.001), IMR (Z=−3.84, p<0.001) and U5MR (Z=−3.84, p<0.001). The ID_isp trends of IMR (Z=−2.2, p=0.027) and U5MR (Z=−2.84, p=0.005) were decreasing, while the ID_isp trends for NMR (Z=+2.19, p=0.028) and CDR (Z=+2.39, p=0.017) were increasing.

Conclusions The results show that at least for IMR and U5MR, in addition to improvement in average national levels, the geographical disparities have decreased. In the cases of NMR and CDR, inspite of the improvements in national levels, the trends of health disparities are not as good. We need to use strategies to provide more specialised care fairly in addition to primary healthcare to reduce disparities in CDR and NMR and influence them more.