Pathways regulating neuronal vulnerability are poorly understood, yet are central to identifying therapeutic targets for degenerative neurological diseases. Here, we characterize mechanisms underlying neurodegeneration in Niemann-Pick type C (NPC) disease, a lysosomal storage disorder characterized by impaired cholesterol trafficking. To date, the relative contributions of neuronal and glial defects to neuron loss are poorly defined. Using gene targeting, we generate Npc1 conditional null mutant mice. Deletion of Npc1 in mature cerebellar Purkinje cells leads to an age-dependent impairment in motor tasks, including rotarod and balance beam performance. Surprisingly, these mice did not show the early death or weight loss that are characteristic of global Npc1 null mice, suggesting that Purkinje cell degeneration does not underlie these phenotypes. Histological examination revealed the progressive loss of Purkinje cells in an anterior-to-posterior gradient. This cell autonomous neurodegeneration occurs in a spatiotemporal pattern similar to that of global knockout mice. A subpopulation of Purkinje cells in the posterior cerebellum exhibits marked resistance to cell death despite Npc1 deletion. To explore this selective response, we investigated the electrophysiological properties of vulnerable and susceptible Purkinje cell subpopulations. Unexpectedly, Purkinje cells in both subpopulations displayed no electrophysiological abnormalities prior to degeneration. Our data establish that Npc1 deficiency leads to cell autonomous, selective neurodegeneration and suggest that the ataxic symptoms of NPC disease arise from Purkinje cell death rather than cellular dysfunction.