The elucidation of the possible mechanism by which carbon nanotube (CNT) could translocate through the glomerular filtration system into the urine by histological TEM in the absence of any probe molecules, was reported. TEM imaging of ultrathin renal cortex sections of BALB/c mice 5 min and 30 min after intravenous administration of MWNTs. The administration of CNT dispersions that were not adequately individualized, or that have aggregated in vivo, could be found in the glomerular capillaries and were not able to translocate through the kidney filtration system. If the injected nanomaterial is in aggregates or bundles, the latter will not be able to cross the glomerular filter and will accumulate in the liver, spleen or lungs. The direct imaging of CNT at the blood-urine interface and their translocation through the glomerular filter, illustrates the mechanism by which novel nanomaterials interact with the biological milieu.