During careful observation of mouse kidney in conventional transmission electron microscopy (TEM) as well as TEM using polyethylene glycol 4000 for embedment-free section instead of Epon and replica TEM of embedment-free sections (for details of the latter method please refer to a paper by Kondo H (Micrsc Res Tech 71:418-442; 2008)), the knot-like structures discrete from the central knots of the diaphragms of fenestrated endothelium were found to occur randomly in the renal glomerular endothelial fenestrae without diaphragms. Those structures were confirmed to be protrusions of underlining basement lamina in conventional TEM using a way of tilting relatively thicker section. The possibility is proposed that the basement lamina randomly forms protrusions directing toward the endothelium, some of which hit the fenestrae, resulting in appearance of concentric or eccentric knots. This feature may have some yet unknown significance in relation to the urine filtration barrier. In addition, the advantage of embedment-free section TEM was repeatedly stressed regarding the transparency to electron beams and 3D viewing of thinly expanded bio-structures.