Economic development is a good achievement to be obtained every region in Indonesia. However, the economic growth, the Human Development Index and agglomeration among the different regions, will eventually lead to inequality and income disparities between regions. The purpose of this research was to analyze effect of the rate of economic growth, HDI and agglomeration on income inequality between regions in Java, Bali and Nusa Tenggara. This research used secondary data panel of time-series data period of 2007-2013 and cross section data 8 Province in Java, Bali and Nusa Tenggara. Whereas the approach FEM ( Fixed Effect Model ) were used to estimate this regression models. The regression results show that the variables economic growth and HDI significant effect on income inequality between regions, whereas agglomeration significant negative effect on inequalities between regions. With the value of R square was 0.7830, it means economic growth, HDI and agglomeration were able to explained economic inequality between regions variations 78,30 percent and 21,7 percent economic inequality between regions can be explained by other variations that were not included in this research analysis model