The datas of Neural Progenitor Cells chip and Embryonic Stem Cells ChIP-Seq from NCBI were analyzed to explore the function of RFX1. A comprehensive analysis showed that RFX1 binding sites spread across each chromosome. Most of them resided in chromosomes 1, 2, 4, 5, 7, 9 and 11, but the least in chromosome Y. And genome wide localization prediction showed that RFX1 binding sites ubiquitously and generally existed throughout the genome. 53.2% of these sequences were distributed in promoter, 22.5 % in the intergentic, 13.1% in the body, and 11.2% in the enhancer in the mouse genome. In addition, the biological processes of RFX1 target genes were analyzed. The majority of the affected biological processes were mainly cellular and metabolic.