POU domain transcription factor Oct-4 plays a crucial role in maintaining self-renewal and pluripotency of embryonic stem (ES) cells in a concentration-dependent manner. However, the molecular mechanism controlling Oct-4 levels in ES cells remains largely unknown. To explore the molecular mechanism regulating Oct-4 function, we constructed a mouse ES cell cDNA library and performed yeast two-hybrid screening using the POU domain of Oct-4 as bait. Here, we present novel evidence for Oct-4 interaction with Ubc9, an E2 conjugation enzyme for SUMO modification, and its modification by SUMO-1. The SUMO acceptor site was identified at lysine residue 118. Importantly, disruption of Oct-4 sumoylation reduced Oct-4 protein stability and self-renewal capacity in ES cells. Interestingly, expression of cYes was found to reduce when Oct-4 sumoylation was disrupted or Oct-4 expression downregulated in ES cells. We further demonstrate that Oct-4 was recruited to the cYes promoter region, suggesting that cYes might be a novel downstream gene of Oct-4. Taken together, we first demonstrate the post-translational modification of endogenous Oct-4 by SUMO and the role of sumoylation in regulating Oct-4 protein stability and function. Our findings provide new evidence for the important role of post-translational modification in controlling Oct-4 function in ES cells.