Squamous cell carcinoma (SCC) and adenocarcinoma (ADC) of the lower esophagus and gastric cardia were compared in their clinical features and long-term prognosis. Two hundred and ninety-five patients with SCC and 263 with ADC were reviewed. Resectability rates for SCC and ADC were 74.2% and 73.2% respectively (P=0.8). Among those who underwent resection, ADC was more advanced, with 22.3% at stage IV compared with 7.4% for SCC (P=0.001). Postoperative cardiac events occurred in 24.2% of SCC patients and 14.7% of ADC patients (P=0.015), and major respiratory complications in 20.1% and 8.6% respectively (P=0.001). Thirty-day mortality rates were 2.7% and 4% (P=0.46), and hospital mortality rates were 11.4% and 7.6% (P=0.19). Median survival rates were 12.5 months for SCC and 11.6 months for ADC (P=0.99) and 5-year survival rates were 19.9% and 17.6% (P=0.55) respectively. Squamous cell carcinoma of the lower esophagus and ADC of the cardia differed in patient demographics and clinical features but long-term prognoses were similar.