Recent RNAi studies have identified many host proteins that modulate virus infection, but siRNA 'off target' effects and the use of transformed cell lines limit their conclusiveness. As murine embryonic stem (mES) cells can be genetically modified and resources exist where many and eventually all known mouse genes are insertionally inactivated, we reasoned that mES cells provided a useful alternative to RNAi screens. Beyond allowing investigation of host-pathogen interactions in vitro, mES cells have the potential to be differentiated into other primary cell types, as well as being used to generate knockout mice for in vivo studies. However, mES cells are poorly characterized for virus infection. To investigate whether embryonic stem cells can be used to explore host-virus interactions, we characterized the responses of mES cells following infection by herpes simplex virus -1 (HSV-1) and influenza A virus. HSV-1 lytically replicates in mES cells although mES cells are less permissive than most other cell types. Influenza virus is able to enter mES cells, express some viral proteins but the replication cycle is incomplete and no infectious virus is produced. Knockdown of the host protein Ahcyl1 in mES cells reduced HSV-1 replication, showing the potential for using mES cells for studying host-virus interactions. Transcriptional profiling, however, indicated the lack of an efficient innate immune response in these cells. Murine ES cells may thus be useful to identify host proteins that play a role in viral replication, but they are not suitable to determine factors that are involved in innate host defense.