To date, all population-based epidemiologic data on gastrointestinal stromal tumor (GIST) in the United States predate the 2001 implementation of GIST-specific histology coding. As such, results from previous studies were limited due to inclusion of non-GIST abdominal or gastrointestinal sarcomas. We utilized a national cancer registry with modern day histological codes to gain greater insight into the true epidemiology of GIST in the United States. We identified 6,142 patients diagnosed with GIST between 2001 and 2011 in the Surveillance, Epidemiology, and End Results database. Incidence, survival, demographic risk factors, and prognostic factors were analyzed. Annual age-adjusted incidence rose from 0.55/100,000 in 2001 to 0.78/100,000 in 2011 and increased with age, peaking among 70-79 year olds (3.06/100,000). GIST was also more common in males than females [rate ratio (RR)=1.35], non-Hispanics than Hispanics (RR=1.23), and blacks (RR=2.07) or Asians/Pacific Islanders (RR=1.50) than whites. The study period had 5-year overall and GIST-specific survival rates of 65% and 79%, respectively. The 5-year overall survival rates for those with localized, regional, and metastatic disease at diagnosis were 77%, 64%, and 41%, respectively. Multivariate analyses demonstrated that older age at diagnosis, male sex, black race, and advanced stage at diagnosis were independent risk factors of worse overall survival. Multivariate analysis also showed the four aforementioned characteristics, along with earlier year of diagnosis, to be independent risk factors of worse GIST-specific survival. As the first population-based, epidemiological study of histologically confirmed disease, our findings provide a robust representation of GIST in the era of immunohistochemical diagnoses.