Most recent studies analyzing candidate biological prognostic factors (including neurotrophin receptor TrkC and proto-oncogene c-MYC) in childhood primitive neuroectodermal brain tumors (PNET) are limited by small patient numbers due to dependence on fresh-frozen tumor material. In contrast, large archives of formalin-fixed, paraffin-embedded PNET samples exist from homogeneously treated patients. The ability of real-time RT-PCR to assay very small mRNA fragments makes this assay amenable to studies where the RNA is moderately or even highly degraded. We have optimized RNA isolation from archive PNET samples and found that TrkC and c-MYC mRNA measurements significantly correlated with those obtained from matching fresh-frozen tissues. Exploitation of already existing archives of formalin-fixed paraffin-embedded PNET samples may accelerate the building of better stratification systems for PNET patients.