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Background Esophageal cancer can be subdivided into two main histological subtypes with significant variability in their etiology and epidemiology. The incidence of esophageal adenocarcinoma (AC) is increasing across the developed countries, whereas the incidence of esophageal squamous cell carcinoma (SCC) is declining. Several risk factors have been identified in the pathogenesis of each subtype, however, their epidemiologic characteristics and distribution throughout Canada remain poorly understood. Methods We performed a retrospective analysis of demographic data across Canada from 1992 to 2010 using two independent population-based cancer registries. The incidence of esophageal cancer, for each subtype, was examined at the levels of provinces/territories, cities, and postal codes. Results A total of 19790 patients were diagnosed with esophageal cancer in Canada between 1992 and 2010; 74% were males. The average national incidence rate was 33.5 cases per million individuals per year. Incidence of esophageal AC increased over time, with notable high-incidence rates on the Vancouver Island, the coasts of the Great Lakes, and the coasts of the Northumberland Strait in the Maritimes. The overall incidence of esophageal SCC has decreased. However, high incidence of esophageal SCC was detected in the Vancouver city, rural eastern Québec, and in the Maritimes. We also report clustering for each subtype using postal codes, which sheds light onto new avenues of research for potential environmental etiologies. Conclusions This study, for the first time, provides a detailed analysis on the burden of esophageal cancer in Canada, revealing important geographic clustering trends.