Cellular stress response and apoptosis are two highly conserved mechanisms for maintaining homeostasis. Hsp60 and Hsp90 have been shown to play pro- and anti-apoptotic roles, respectively. Our present study examined whether there is a correlation between the expression of Hsp60 and Hsp90, clinical parameters, the apoptotic index (AI), and the prognosis of patients with oesophageal squamous cell carcinoma (ESCC). We immunohistochemically stained cells for Hsp60, Hsp90, and single-stranded DNA (ssDNA), which acts as an apoptotic marker. In normal oesophageal epithelium tissue, Hsp60 and Hsp90 were expressed in the cytoplasm and membrane from the basal cell layer to the supra-basal cell layers. Hsp60 and Hsp90 positive stainings (+) were found in 63 of 123 cases (51%) and 62 of 123 cases (50%), respectively. There was no correlation between Hsp60 and Hsp90 expression levels and any of the clinical parameters examined. The five-year survival rate for ESCC patients with Hsp60 (+) expression was significantly higher than for those patients with Hsp60 (-) expression (P=0.0371). Five-year survival rates of patients with Hsp60 (+) and (-) were 49% and 33%, respectively. By contrast, Hsp90 expression failed to predict patient prognosis (P=0.7965). The high-AI group did not have a significantly better prognosis than the low-AI group (P=0.2218). Statistical analysis showed a significant correlation between the expression of Hsp60 and AI in ESCC patients (P=0.008). Thus, the five-year survival rate for the high-AI/Hsp60 (+) group was statistically significantly better than for the other groups (P=0.0281). The results obtained in this study indicate that positive Hsp60 expression is a good prognostic indicator. This may be due to its role as a chaperone in contributing to the induction of apoptosis. These data suggest that Hsp60 expression correlates with the AI and patient prognosis in human ESCC.