AbstractBackgroundChildhood germ cell tumors (cGCTs), believed to arise from transformed primordial germ cells by an unknown mechanism, provide a unique model system for investigating cell signaling, pluripotency, and the microenvironment of neoplastic stem cells (NSCs) in vivo. This is the first report of proteomics of cGCTs.ProcedureFour dysgerminomas (DYSs) and four childhood endodermal sinus tumors (cESTs), resembling self‐renewing and differentiating NSCs, respectively, were selected. Proteomic studies were performed by 2‐DE, SDS–PAGE, and cLC/MS/MS with protein database searching.Results2‐DE: 9 of 941 spots were differentially regulated with greater than a twofold change in spot volume for at least three of four gels in each group. Two of nine spots had P values for the t‐test analysis of comparisons less than 0.001, while the remaining spots had P values from 0.013 to 0.191. Top‐ranked proteins were identified in nine of nine spots with 4.0–38% sequence coverage. APOA1, CRK, and PDIA3 were up‐regulated in cESTs. TFG, TYMP, VCP, RBBP, FKBP4, and BiP were up‐regulated in DYSs. SDS–PAGE: Up‐regulation of NF45 and FKBP4 was observed in four of four cESTs and DYSs, respectively. The fold‐changes observed correspond with characteristic genetic changes.ConclusionDifferential regulation of FKBP4 and NF45, combined with previous research on immunosuppressant binding, suggests that glucocorticoid receptor signaling merits further investigation in cGCTs and NSCs. Pediatr Blood Cancer 2012; 58: 722–728. © 2011 Wiley Periodicals, Inc.