Bacterial magnetosomes (BMs) have drawn great interest as novel magnetic targeted carriers and have been widely used as carriers for enzymes, nucleic acids and antibodies experimentally. However, BMs have rarely been employed as drug carriers in vivo mainly due to the unclear biocompatibility and pharmacokinetics of BMs. In this study, we provided a unique effective method for purification and sterilization of BMs. The BMs obtained exhibited sterility, high purity, narrowed size-distribution, uniformity in morphology, intact membrane and abundant amino groups in BMs membrane. To elucidate the in vivo body distribution of BMs and if BMs displayed any rejection by animals when they are delivered into the vascular system, the BMs were injected into the sublingual vena of Sprague-Dawley (SD) rats and the tissue distribution of BMs in dejecta, urine, serum and main organs was examined. A target distribution of BMs in SD rats was observed. After injected into the sublingual vena, BMs were only found in livers and there was no obvious evidence to indicate the existence of BMs in the dejecta and urine within 72 h following the intravenous administration.