Several recent studies have suggested that mouse embryonic stem cells (ESCs) can differentiate into female and male germ cells in vitro. The meiotic process in germ cell-like cells derived from ESCs has not been studied in detail, but it has been reported that synaptonemal complex protein-3 (SYCP3) is expressed in these cells. Here, we have carefully evaluated the meiotic process in germ cell-like cells derived from ESCs, using a panel of meiosis-specific markers that identify distinct meiotic signatures unique to meiotic prophase I development in vivo. We find that whereas SYCP3 is expressed in germ cell-like cells, other meiotic proteins, such as SYCP1, SYCP2, STAG3 (stromal antigen 3), REC8 (meiotic protein similar to the rad21 cohesins), and SMC1 (structural maintenance of chromosomes-1)-beta, are not expressed. The nuclear distribution of SYCP3 in the germ cell-like cells is highly abnormal and not associated with the chromosomes of these cells. Fluorescence in situ hybridization analysis shows that the SYCP3-positive germ cell-like cells do not contain synapsed homologous chromosomes but instead display a chromosomal organization normally found in somatic cells. The absence of expression of essential meiotic proteins and a normal meiotic chromosomal organization strongly suggests that the germ cell-like cells formed from ESCs fail to progress through meiosis.