Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. So far, surgical resection has been the only curative treatment, but new options became available with the application of imatinib (Glivec) as a specific molecular inhibitor. Even after complete resection, GISTs have a high rate of recurrence and disease-linked mortality. Here we report on the case of a clinically well 57-year-old woman who presented to us 3 years after resection of a GIST of the small intestine. Abdominal ultrasound and CT scan showed intestinal wall thickening in the area of anastomosis and mesenteric lymphadenopathy, suggesting a recurrence of the primary GIST. However, serological testing was positive for yersinia antibodies. Surgical exploration revealed an asymptomatic infection with Yersinia enterocolitica serotype O9, proven by positive culture and histology, which showed no evidence of malignancy. Prognostic variables for GIST as well as diagnostic measures and limitations for yersiniosis are discussed. In the end, only surgical exploration and histological analysis could establish the final diagnosis. In conclusion, GISTs have a high likelihood of recurrence even after complete resection, but an asymptomatic infection such as yersiniosis must be considered as a differential diagnosis to GIST recurrence.