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Thymoma is one of the most common solid tumors in the mediastinum. Because there is no typical cell line for human thymoma, the development and use of molecular‐based therapy for thymoma will require detailed molecular‐genetic analysis of patients' tissues. Recent reports showed that genetic aberrations in thymoma were most frequently seen in chromosome 6q regions. We investigated the use of oligonucleotide arrays to monitor in vivoexpression levels of genes in chromosome 6 regions in early‐(stage I or II) and late‐ (stage IVa) stage thymoma tissues from patients. These in vivogene expression profiles were verified by real‐time quantitative reverse transcription polymerase chain reaction (RT‐PCR) using LightCycler for 48 thymoma patients and sandwich ELISA for 33 thymoma patients. Using both methods, a candidate gene was identified which was overexpressed in stage IV thymoma. This was a known glycosylphosphatidyl inositol (GPI)‐anchored protein (GPI‐80), which is highly homologous with Vanin‐1, a mouse thymus homing protein. Serum level of GPI‐80 was confirmed to be elevated in stage IV thymoma compared with in stage I thymoma by using sandwich ELISA. The combined use of oligonucleotide microarray, real‐time RT‐PCR, and ELISA analyses provides a powerful new approach to elucidate the in vivomolecular events surrounding the development and progression of thymoma.