Progressive myoclonus epilepsy of Unverricht-Lundborg type (EPM1) is a hereditary neurodegenerative disorder caused by mutations in the cystatin B (CSTB) gene encoding an inhibitor of cysteine proteases. Here, we provide the first detailed description of the onset and progression of pathologic changes in the CNS of Cstb-deficient (Cstb) mice. Our data reveal early and localized glial activation in brain regions where neuron loss subsequently occurs. These changes are most pronounced in the thalamocortical system, with neuron loss occurring first within the cortex and only subsequently in the corresponding thalamic relay nucleus. Microglial activation precedes the emergence of myoclonia and is followed by successive astrocytosis and selective neuron loss. Neuron loss was not detected in thalamic relay nuclei that displayed no glial activation. Microglia showed morphologic changes during disease progression from that of phagocytic brain macrophages in young animals to having thickened branched processes in older animals. These novel data on the timing of pathologic events in the CSTB-deficient brain highlight the potential role of glial activation at the initial stages of the disease. Determining the precise sequence of the neurodegenerative events in Cstb mouse brains will lay the basis for understanding the pathophysiology of EPM1.