The nanocavitation distribution in deformed High Density PolyEthylene (HDPE) was investigated. A flat notched sample of HDPE, deformed under steady crosshead speed up to the end of the stress softening, was observed by classical synchrotron parallel beam microtomography and magnified holotomography with a true spatial resolution of 0.7 μm and 0.05 μm, respectively. Image processing, 3D image segmentation and 2D-Fast Fourier Transform, was shown to lead to quantification of void volume fraction and void size distributions. Nanocavitation morphology and distribution in HDPE reveal to be similar to cavitation mechanisms in other semi-crystalline polymers, but at a different scale. While a slight decrease of the void diameter was seen, from the end of the neck shoulder to the extended neck region, a significant increment of the height was evidenced. Furthermore, the results provide compelling evidence of morphology transition of cavities within the test sample from an oblate to a prolate geometry.