Background: Hepatocellular carcinoma (HCC) is one of the most vascularized tumor types, and is characterized by development of heterogeneous immature vessels with increased permeability. Here, we analyzed morphology and vascular permeability-related structures in endothelial cells of HCC microvessels. Methods: Small (Type I) and large (Type II) peritumoral blood microvessels were assessed in HCC-bearing mice. By transmission electron microscopy, endothelial cell cytoplasm area, free transport vesicles, vesiculo-vacuolar organelles and clathrin-coated vesicles were measured. Results: The phenotypic changes in the HCC microvessels included presence of sinusoidal capillarization, numerous luminal microprocesses and abnormal luminal channels, irregular dilatations of interendothelial junctions, local detachment of basement membranes and widened extracellular space. Endothelial cells Type I microvessels showed increased vesicular trafficking-related structures. Conclusion: Ultrastructural characteristics of microvessels Type I can associate with HCC new-formed microvessels. The morphological changes observed in HCC microvessels might explain the increased transcellular and paracellular permeability in HCC endothelial cells.