Germ cell tumors (GCT) comprise a heterogeneous group of benign and malignant tumors. Based on their different biological characteristics and their origin, five types of GCT are classified. Among these, malignant seminomatous and non-seminomatous GCT in males and females are designated as type II GCT. They occur most frequently as malignant testicular GCTs. Many characteristics of type II GCT can be linked to embryonic stem cells. Intratubular germ cell neoplasia, unclassified (IGCNU) is the precursor of type II GCT and derives from undifferentiated germ cells, gonocytes, which persist in the newborn testis and escape the normal differentiation process. It is suggested that Exon-17-activated mutations of the receptor tyrosine kinase, c-KIT, occur early in germ cell development and that gonocytes with an activated c-KIT receptor are restricted in their differentiation, thereby escaping normal development. New diagnostic markers for neoplastic germ cells, including OCT3/4 and AP-2gamma, are specifically detected in IGCNU, seminomas and embryonal carcinomas and are helpful in the differentiation of type II GCT from other malignant tumors.