Background: Adolescent and young adults (AYAs) who develop gastrointestinal (GI) cancer are rare and have unique needs. There is limited literature defining the epidemiology of malignant disease across the entire GI tract in this age group. The objective of this study was to explore incidence and survival trends in the United States for all types of GI cancers in AYAs compared to older adults. Methods: We analyzed all incident cases of GI tract cancers in AYAs aged 15 to 39 and older adults aged 40 to 64 in the National Cancer Institute Surveillance, Epidemiology and End Results (SEER) program 2000-2013 database. For each age group and sex, we determined incidence rates, temporal changes in incidence, overall prognosis and stage-based prognosis for all primary tumor sites throughout the GI tract. Results: The incidence of colorectal cancer (CRC) distal to the splenic flexure has increased in AYAs whereas all CRC has decreased in older adults. We found that compared to older adults, AYAs have experienced better survival for most cancers arising at or proximal to the cecum regardless of stage. Conversely, more distal tumors were associated with worse prognosis in AYAs for regional or distant-stage disease. For distal CRC, the greatest age-based discrepancy in survival occurred for regional disease. Despite decreasing incidence of anal cancer in AYAs, young females have experienced worse survival with this disease compared to AYA males and older adults. Conclusions: We have identified age and gender-based disparities in survival relating to GI cancers. Rising rates of distal CRC in AYAs highlight the need for further exploration of molecular mechanisms and potential therapeutic targets for these malignancies which are also associated with worse survival in the younger population.