One of the major problems in the treatment of squamous cell carcinoma of the oesophagus (ESCC) is the unresponsiveness to cytotoxic drugs. So far, the mechanisms underlying the intrinsic drug resistance of ESCC remain unclear. The aim of this study was to determine the role of the newly recognised drug resistance protein, the multidrug resistance protein (MRP), in ESCC drug resistance. Tumour biopsies from ESCCs were analysed by RNase protection assay (RPA) as well as by immunohistochemistry (IHC) for the presence of MRP mRNA or protein, respectively. The ESCC samples were obtained from patients participating in a prospective randomised clinical phase III trial, evaluating pre-operative chemotherapy (cisplatin and etoposide) followed by surgery versus surgery alone in patients with operable ESCC. For most patients, tumour biopsies taken at diagnosis by endoscopy as well as surgically resected primary tumours were available. Of 58 ESCC patients enrolled, 28 received chemotherapy before surgical resection of their tumours, and 30 were treated with surgery alone. 12 patients (3 complete and 9 partial responses; 43%) showed a major response after chemotherapy, 10 patients (36%) had stable disease (SD), and 6 (21%) progressive disease (PD). On 14 surgically resected, untreated, primary ESCCs, the IHC scores correlated with the MRP mRNA levels, quantitated by RPA (multiple testing, P < 0.01). MRP expression was detected by IHC in the vast majority (52/58; 90%) of the diagnostic biopsies. MRP expression did not differ significantly between CR + PR, and patients with SD or PD. In addition, multivariate analysis by logistic regression did not show any effect of tumour cell differentiation or UICC tumour stage on the outcome of pre-operative chemotherapy in relation to MRP expression. However, a difference became apparent (Sign-test, P < 0.05) for higher MRP expression in tumours from patients with PR or SD, when comparing MRP levels in paired tumour samples before and after chemotherapy, suggesting that chemotherapy selected for drug-resistant cell clones.