We determined the distribution and biocompatibility of graphene oxide (GO) in mice by using radiotracer technique and a series of biological assays. Results showed that GO was predominantly deposited in the lungs, where it was retained for a long time. Compared with other carbon nanomaterials, GO exhibited long blood circulation time (half-time 5.3 ± 1.2 h), and low uptake in reticuloendothelial system. No pathological changes were observed in examined organs when mice were exposed to 1 mg kg−1 body weight of GO for 14 days. Moreover, GO showed good biocompatibility with red blood cells. These results suggested that GO might be a promising material for biomedical applications, especially for targeted drug delivery to the lung. However, due to its high accumulation and long time retention, significant pathological changes, including inflammation cell infiltration, pulmonary edema and granuloma formation were found at the dosage of 10 mg kg−1 body weight. More attention should be paid to the toxicity of GO.Graphical abstractResearch highlights► GO can be effectively labeled with 188Re. ► 188Re–GO was predominantly deposited in the lungs. ► GO shows good biocompatibility to targeted organs. ► GO shows good biocompatibility to RBC. ► Provided basic information for toxicity assessment and biomedical applications.