Huntington's disease (HD) is a progressive neurodegenerative disorder that generally begins in middle age with abnormalities of movement, cognition, personality, and mood. Neuronal loss is most marked among the medium-sized projection neurons of the dorsal striatum. HD is an autosomal dominant genetic disorder caused by a CAG expansion in exon 1 of the HD gene, encoding an expanded polyglutamine (polyQ) tract near the N-terminus of the protein huntingtin. Despite identification of the gene mutation more than a decade ago, the normal function of this ubiquitously expressed protein is still under investigation and the mechanisms underlying selective neurodegeneration in HD remain poorly understood. Detailed postmortem analyses of brains of HD patients have provided important clues, and HD transgenic and knock-in mouse models have facilitated investigations into potential pathogenic mechanisms. Subcellular fractionation and immunolocalization studies suggest a role for huntingtin in organelle transport, protein trafficking, and regulation of energy metabolism. Consistent with this, evidence from vertebrate and invertebrate models of HD indicates that expression of the polyQ-expanded form of huntingtin results in early impairment of axonal transport and mitochondrial function. As well, alteration in activity of the N-methyl-d-aspartate (NMDA) type glutamate receptor, which has been implicated as a main mediator of excitotoxic neuronal death, especially in the striatum, is an early effect of mutant huntingtin. Proteolysis and nuclear localization of huntingtin also occur relatively early, while formation of ubiquitinated aggregates of huntingtin and transcriptional dysregulation occur as late effects of the gene mutation. Although each of these processes may contribute to neuronal loss in HD, here we review the data to support a strong role for NMDA receptor (NMDAR)-mediated excitotoxicity and mitochondrial dysfunction in conferring selective neuronal vulnerability in HD.