The purpose of this study was to clarify the clinical implications of thymic fluorodeoxyglucose (FDG) uptake after chemotherapy in pediatric patients with malignant disease. Twenty-two pediatric patients, aged 0-17 years (mean 7.0 years), who had undergone FDG positron emission tomography (PET) were examined retrospectively. A total of 48 FDG-PET scans of the 22 patients were reviewed. Seven PET scans were recorded before the initial chemotherapy, and the remaining 41 scans were conducted during and after chemotherapy. Thymic FDG uptake was evaluated using standardized uptake value (SUV) analysis. The effect of chemotherapy on thymic FDG uptake was assessed by comparing SUV before, during, and after chemotherapy. The change in thymic FDG uptake with increasing time after the completion of chemotherapy was also assessed. Clinical laboratory data including number of white blood cells (WBCs), erythrocytes (RBCs), platelets, plasma glucose level and differential white blood count were analyzed for their association with thymic FDG uptake. Thymic FDG uptake in patients during chemotherapy was significantly lower than that in patients before chemotherapy (mean+/-SD 1.71+/-0.48 vs 2.27+/-0.32, respectively, P<0.01). Thymic FDG uptake in patients after chemotherapy was significantly higher than that in patients during chemotherapy (mean+/-SD 2.74+/-0.70 vs 1.71+/-0.48, respectively, P<0.01). A significant relationship between thymic FDG uptake and interval after completion of chemotherapy (r=0.74, P<0.0001) was observed. Significant relationships between blood counts (WBCs, RBCs, and platelets) and thymic FDG uptake were also observed. Comparison of the differential white blood count and thymic FDG uptake revealed a significant relationship only with lymphocyte count. Thymic FDG uptake in pediatric patients after completion of chemotherapy should not be mistaken as recurrent or metastatic thymic malignancy. Thymic FDG uptake appears to be associated with thymic function or hematopoietic function in bone marrow. Interpretation of FDG-PET must be made with this consideration in mind.