Seminomas are characterized by expression of several stem cell markers, supporting their origin from germ cells. The current study focuses on novel germ cell markers in normal testes compared to those in fetal testes and different progression stages of seminomas. Microarray data were followed by RT-PCRs and immunohistochemistry on pure seminomas (pT1 to pT3) compared to adult and fetal testis. An upregulation of known germ cell markers, KIT, OCT4 and NANOG, was confirmed in seminoma specimens. We also identified novel germ cell markers such as BOB1 (POU2AF1, OBF1) and prominin 1 (PROM1, CD133), which were significantly upregulated in seminoma specimens, compared to normal testes. Furthermore, two Sertoli cell markers, SCGF (SCF) and the newly identified neuronal stem cell factor, MCFD2 (SDNSF), were expressed in seminoma cells. While BOB1 was expressed in fetal testis of second and third trimester of gestation, MCFD2 and PROM1 were only present in gonocytes up to the second trimester. All marker genes investigated were not further regulated in progressing tumour stages between pT1 and pT3. In conclusion, the germ cell markers described here provide evidence for the origin of seminoma cells, which could be from the developmental stage of early gonocytes or from spermatogonia re-expressing markers of the developing germ cells.