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Pathological complete response (pCR) after chemoradiotherapy (CRT) is the best predictor of survival in patients with squamous cell carcinoma (SCC) of the esophagus. Although no adjuvant treatment is recommended for individuals who achieve pCR, approximately 30% of these patients develop a recurrence. We applied an immunohistochemistry (IHC) stain on resected lymph nodes to evaluate the incidence of lymph node micrometastases (LNMs) and its prognostic significance.Between 1995 and 2004, paraffin-embedded specimens for evaluating the presence of LNM were available for 52 pCR patients. We performed IHC staining with the cytokeratin antibody AE1/AE3 on resected lymph nodes and correlated the pathological findings to cancer recurrence and survival.A total of 510 lymph nodes from 52 patients were examined. The incidence of LNM in pathological complete responders after CRT was 11.5%. Only six patients were found to have AE1/AE3-positive cells in the IHC staining. However, patients with LNM had a higher recurrence rate (50% vs. 22%, P=0.16) and a reduced disease-free survival rate (44% vs. 75%, P=0.16). Patients with LNM had a 3.6-fold higher probability to develop recurrence compared with those without LNM (P=0.15).LNMs are uncommon in pathological complete responders but hold prognostic significance.