Background: Pathological examination combined with tumor markers has become a standard for the diagnosis of intracranial germ cell tumors (ICGCTs), but the current concept of 'secreting germ cell tumors' and three empirically highly specific diagnostic criteria (beta-hCG >= 50 IU/L or alpha FP >= 10 ng/mL; beta-hCG >= 100 IU/L or alpha FP >= 50 ng/mL; beta-hCG > 50 IU/L or alpha FP > 25 ng/mL) are not based upon pathology examination or CSF cytology. Further investigation is needed to re-evaluate their value. Methods: A multidisciplinary diagnostic team was created. Valid beta-hCG/alpha FP data were collected from cases of ICGCTs confirmed by pathology and CSF cytology (n = 58) between 1991 and 2012, and from suspected ICGCTs cases (n = 17) between 2011 and 2012 as controls [Langerhans cell histiocytosis (LCH), n = 12; and other intracranial tumor (ICT), n = 5]. The cut-off points for beta-hCG and alpha FP were calculated using receiver operating characteristic (ROC) curves. Results: This study clarifies the relative rationality of one criteria (beta-hCG > 50 IU/L and alpha FP > 25 ng/mL); confirms new beta-hCG diagnostic cut-off points: CSF beta-hCG >= 8.2 IU/L and serum beta-hCG >= 2.5 IU/L (sensitivity of 47 and 34 %, respectively, specificity of 100 %, both; P < 0.05); and empirically adjusts the criteria for alpha FP to >= 3.8 ng/mL in CSF and to >= 25 ng/mL in serum. The total diagnostic sensitivity for ICGCTs finally increased from 34.6 to 65.4 % (P < 0.05, diagnostic value of CSF beta-hCG exceeds 90 %). Subtype diagnosis improved with alpha FP in 16.7 % of non-geminomatous germ cell tumor cases. Conclusion: New evidence-based criteria of beta-hCG and alpha FP can help improving early and formal diagnosis of ICGCTs, and is of great clinical significance.