We estimated the effect of the Harderian gland (an orbital gland of land vertebrates) on the measurement of cerebral metabolic rate of glucose (CMRGIc) of the rat brain using positron emission tomography (PET) for animal use. The Harderian gland had the high accumulation of 18-F labeled deoxyglucose (FDG) after intravenous injection. By placing the large regions of interest (ROI) (twice the full width at half maximum in diameter), the CMRGIc in the frontal region was slightly higher compared with the CMRGIc after Harderian gland resection, but the parietal and occipital regions and the cerebellum had the similar level of CMRGIc before and after Harderian gland resection. Therefore the Harderian gland has a slight effect on the frontal lobe CMRGIc, but such overestimation can be within the permissible range for PET study of rat brains.