In spite of endoscopic surveillance programs, 90% of patients initially presenting with Barrett's carcinoma have locally advanced disease. In these patients, preoperative chemotherapy increases the chance of a curative resection in responding patients. Unfortunately, response occurs in only 50% of patients after chemotherapy with cisplatin, 5-fluorouracil and leucovorin. Response prediction seems to be possible by measuring metabolic activity by positron emission tomography (PET) scan. Differentiation of responders from non-responders even before starting chemotherapy might be possible using microarray technology and immunhistology in tumour biopsies. A pattern of at least two-fold differentially regulated genes comparing responding and non-responding oesophageal adenocarcinomas was identified. The strongest difference can be seen for tumour necrosis factor, polyribonucleotide nucleotidyltransferase and the ephrin-B3-receptor. In conclusion, our experience suggests that it may be possible to characterize patients responding to chemotherapy by PET two weeks after starting the chemotherapy or even before treatment using customized microarray analysis.