Germ cells are the 'ultimate stem cells' in that they are the precursors of the gametes and are, therefore, capable of generating an entirely new organism at fertilisation. In mice, germ cells are set aside from somatic cells at 7.25 days post coitum (dpc), are characterised by continued expression of core pluripotency genes (Oct4, Sox2, Nanog) and migrate through the embryo to colonise the developing gonads by 10.5–11.5 dpc. Upon entering the developing ovaries, germ cells initiate prophase of meiosis I by 13.5 dpc in response to retinoic acid (RA) in the somatic environment. In contrast, the developing testis degrades RA and produces the male-specific signaling molecules Fgf9 and Nodal such that the germ cells avoid entering meiosis and undergo G0/G1 mitotic arrest by 14.5 dpc. Using expression screening approaches we found that the developmentally conserved homeobox transcription factors Lhx1 and Otx2 are both expressed specifically in male germ cells from 12.5 to 13.5 dpc. Interestingly, others have shown that Lhx1 and Otx2 are expressed in a wide variety of tissues exposed to Fgf and Nodal signaling during fetal development, and have been shown to interact and cooperate in instructing formation of the embryonic head. We examine the effects of germ cell-specific loss of Lhx1 and/or Otx2 on expression of core pluripotency genes and previously identified late male germ cell fate markers (Nanos2 and Dnmt3L) to determine the novel roles of these transcription factors in driving male germ cell fate.