It has been reported that F18-fluorodeoxyglucose (FDG) uptake in the neck and supraclavicular lesions represents activated brown adipose tissue (BAT). In the present study, the association between BAT activity, detected by FDG-positron emission tomography (PET), and the clinicopathological features of patients with breast cancer was investigated. The cases of 156 consecutive patients with breast cancer who underwent FDG-PET preoperatively were analyzed. The distribution and intensity of atypical FDG uptake in the neck and/or supraclavicular region was reviewed. The intensity was graded as follows: 1, weak; 2, moderate; and 3, intense. Among the 156 patients, 70 (44.9%) exhibited grade 1 intensity, 65 (41.7%) exhibited grade 2 intensity and 21 (13.5%) exhibited grade 3 intensity. The intensity of FDG was significantly associated with human epidermal growth factor receptor 2 (HER2) expression and progesterone expression. Among the 156 patients, 6 (3.8%) had recurrent disease. Multivariate analysis revealed that showing a low grade of atypical FDG uptake was the only independent risk factor of short-term recurrence, and none of the patients with recurrent disease had atypical FDG uptake that may reflect the activation of BAT. These results indicated that the presence of BAT is associated with HER2 expression and the absence of BAT may be a prognostic factor for breast cancer.