BACKGROUND: The objective of the present population-based analysis was to assess survival patterns in patients with resected and metastatic GIST. METHODS: Patients with histologically proven GIST were extracted from the Surveillance, Epidemiology and End Results (SEER) database from 1998 through 2011. Survival was determined applying Kaplan-Meier-estimates and multivariable Cox-regression analyses. The impact of size and mitotic count on survival was assessed with a generalized receiver-operating characteristic-analysis. RESULTS: Overall, 5138 patients were included. Median age was 62 years (range: 18-101 years), 47.3% were female, 68.8% Caucasians. GIST location was in the stomach in 58.7% and small bowel in 31.2%. Lymph node and distant metastases were found in 5.1 and 18.0%, respectively. For non-metastatic GIST, three-year overall survival increased from 68.5% (95 % CI: 58.8-79.8%) in 1998 to 88.6% (95 % CI: 85.3-92.0%) in 2008, cancer-specific survival from 75.3% (95 % CI: 66.1-85.9%) in 1998 to 92.2% (95 % CI: 89.4-95.1%) in 2008. For metastatic GIST, three-year overall survival increased from 15.0% (95 % CI: 5.3-42.6%) in 1998 to 54.7% (95 % CI: 44.4-67.3%) in 2008, cancer-specific survival from 15.0% (95 % CI: 5.3-42.6%) in 1998 to 61.9% (95 % CI: 51.4-74.5%) in 2008 (all PTrend < 0.05). CONCLUSIONS: This is the first SEER trend analysis assessing outcomes in a large cohort of GIST patients over a 11-year time period. The analysis provides compelling evidence of a statistically significant and clinically relevant increase in overall and cancer-specific survival from 1998 to 2008, both for resected as well as metastatic GIST.