AbstractIncreased MYCN gene copy number is a characteristic property of neurogenic tumors. Fluorescence in situ hybridization (FISH) and array‐based comparative genomic hybridization (array‐CGH) are traditionally used to determine MYCN amplification for tumor stratification. A unique ability of real‐time quantitative polymerase chain reaction (qPCR) to determine gene copy number, even within a small percent of observed tumor cells, and can be more appropriate. MYCN genomic copy number from 44 human brain tumors (22 medulloblastomas and 22 neurocytomas) was determined by means of FISH, array‐CGH, and qPCR. By qPCR, with the original set of oligonucleotides, 17 out of 44 (38.6%) tumors were found to contain a 1.3‐ to 2.9‐fold increase of MYCN defined as low‐level gain. An absolute qPCR method was used to get high accuracy of results. Strong correlation was observed between the three methods: for medulloblastomas, r=1 (P<0.01) between FISH and array‐CGH and r=0.92 (P<0.01) between qPCR and FISH/array‐CGH. For neurocytomas, r=0.9 (P<0.01) between FISH and array‐CGH and r=0.34/0.43 (P<0.01) between qPCR and FISH/array‐CGH. Absolute qPCR assays possess high precision compared to other conventional methods and can be used for accurate and quickness detection of MYCN status (low‐level gene gain and amplification). J. Clin. Lab. Anal. 22:123–130, 2008. © 2008 Wiley‐Liss, Inc.