We have constructed cDNA libraries representing transcripts from purified populations of germ cells and of somatic cells, isolated from fetal mouse gonads at 12.5 days postcoitum (dpc). We have used these libraries to study differential gene expression in fetal germ cells on the basis of differential representation of specific cDNAs in each library. We show that in addition to expression of housekeeping genes at expected levels, four genes responsible for germ cell-specific phenotypes are expressed at significantly different levels in germ cells and surrounding somatic cells. These include tissue-nonspecific alkaline phosphatase (tnAP), transcription factor Oct-3/4, the c-kit proto-oncogene, and DNA methyltransferase (Mt). The significance of these results is discussed in the context of events contributing to early development of germ cells. It is concluded that fetal germ cells appear to retain a pattern of gene expression resembling that in early pluripotent embryonic cells, and that this may be important for the maintenance of genetic totipotency.