Runt related transcription factors (RUNX), a family of well-known transcription factors, play key regulatory roles in diverse biological processes, such as proliferation, differentiation, and DNA repair. Of RUNX family, RUNX3 is the least well characterized of the three family members. Nevertheless, the role of RUNX3 as a key regulator in essential biological pathways has been reported and inactivation of RUNX3 leads to a variety of disease, such as cancer, via regulation of Wnt signaling and K-ras mutations in many mammalian tissues. Recent studies using RUNX3-deficient cells and mice revealed an association with hematopoiesis and hypersensitivity to granulocytecolony stimulating factor. Nevertheless, protein dynamics associated with RUNX3 remain poorly understood. In the present study, we performed a large-scale protein study from Runx3 knockout (KO) mouse embryonic stem cells (mESC) using a stable isotope labeling by amino acids (SILAC)-based quantitative proteomics approach. The results showed that 67 proteins were significantly up and downregulated after Runx3 KO. Bioinformatic analyses that revealed that these proteins have diverse biological functions, such as substances transport and cellular structure. Thus, our results enhance our current understanding of the function of RUNX3 in mESCs and suggest potential roles for RUNX proteins in diverse diseases. Additionally, our results can be used as a database to help us understand the mechanism of action of RUNX3.