BACKGROUND:The incidence, treatment and outcome of patients with newly diagnosed gastrointestinal stromal tumour (GIST) were studied in an era known for advances in diagnosis and treatment. METHODS:Nationwide population-based data were retrieved from the Netherlands Cancer Registry. All patients with GIST diagnosed between 2001 and 2012 were included. Primary treatment, defined as any treatment within the first 6-9 months after diagnosis, was studied. Age-standardized incidence was calculated according to the European standard population. Changes in incidence were evaluated by calculating the estimated annual percentage change (EAPC). Relative survival was used for survival calculations with follow-up available to January 2017. RESULTS:A total of 1749 patients (54·0 per cent male and median age 66 years) were diagnosed with a GIST. The incidence of non-metastatic GIST increased from 3·1 per million person-years in 2001 to 7·0 per million person-years in 2012; the EAPC was 7·1 (95 per cent c.i. 4·1 to 10·2) per cent (P < 0·001). The incidence of primary metastatic GIST was 1·3 per million person-years, in both 2001 and 2012. The 5-year relative survival rate increased from 71·0 per cent in 2001-2004 to 81·4 per cent in 2009-2012. Women had a better outcome than men. Overall, patients with primary metastatic GIST had a 5-year relative survival rate of 48·2 (95 per cent c.i. 42·0 to 54·2) per cent compared with 88·8 (86·0 to 91·4) per cent in those with non-metastatic GIST. CONCLUSION:This population-based nationwide study found an incidence of GIST in the Netherlands of approximately 8 per million person-years. One in five patients presented with metastatic disease, but relative survival improved significantly over time for all patients with GIST in the imatinib era.