Gastrointestinal stromal tumours (GIST) are identified by their specific morphology added with immunohistochemical staining with anti-CD117, the phenotypic marker for GIST in the majority of cases. In this study the reported incidence of GIST and GST-like tumours before and after the routine availability of the specific diagnostic marker CD117 antigen was investigated. All patients with GIST or GIST-like tumours were selected from PALGA, a nation-wide network and registry of histo- and cytopathology in the Netherlands, to calculate the incidence in 1995 and longitudinally over time between 1998 and 2003. Pathological reports were retrieved to assess the type of immunostaining used and to assess the risk category for malignant behaviour accordingto the recently published consensus criteria. The annual incidence of GIST as distilled from the national pathology registry increased from 2.1 per million inhabitants in 1995 to 12.7 per million inhabitants in 2003. The incidence of GIST-like tumours decreased from 17.6 per million inhabitants in 1995 to 12.7 per million inhabitants in 2003. The incidences were stable from 2000 onwards. Additional analysis in 2003 indicated that more than 90% of the GIST tested was CD117 positive, compared to only 4% of the GIST-like tumours. Almost 50% of the GIST was considered to be at high-risk for malignant behaviour, according to the consensus criteria. The increased incidence of GIST 1995-2003 is related to increased understanding of GIST pathobiology and the routine availability of the diagnostic immunohistochemical antibody directed against the CD117 antigen.