This paper investigates the changes in income inequality and poverty in Japan between 1994 and 2009, using the National Survey of Family Income and Expenditure. Although there are voluminous literature in Japan, which investigate the trends of poverty and inequality, most of their analysis don’t rely on statistical inference. In addition, even with large sample micro-data, the sample size for subgroup (i.e. household type, area, etc.) is relatively small, which leads to larger standard errors and wider confidence intervals. So this study estimates the standard errors and confidence intervals of inequality and poverty indices, using bootstrap method. Two major results are shown. One is that the increases of inequality and poverty indices between 1994 and 2009 are statistically significant. The other one is that since the standard errors are relatively large for prefecture-level estimates and most of the confidence intervals are overlapped among prefectures, it is not necessarily adequate to compare their computed values of income inequality and poverty.