Hepatic encephalopathy (HE) is a neurocognitive syndrome associated with liver disease, presenting a spectrum of neuropsychiatric abnormalities ranging from mild cognitive impairment to severe disorientation, coma, and potentially death. Traditionally considered a gliopathy affecting astrocytes without neuronal damage, recent evidence suggests a neurodegenerative component in HE pathogenesis. Studies have shown cerebellar neurodegeneration in HE and chronic liver disease, highlighting the need for robust methods to estimate cerebellar neuron numbers to better understand HE’s neurological impact. Unbiased stereology, the gold standard for quantifying biological objects within three-dimensional structures from two-dimensional tissue images is crucial in this context. This protocol documents a biological application of computerized stereology to estimate the total number of Purkinje neurons in the mouse cerebellum, thereby enhancing our understanding of neurodegenerative processes in HE.