Background: Huntington's disease (HD) is a dominantly inherited neurodegenerative disorder that affects cognitive and motor abilities by primarily targeting the striatum and cerebral cortex. HD is caused by a mutation elongating the CAG repeats within the Huntingtin gene, resulting in HTT protein misfolding. Although the genetic cause of HD has been established, the specific susceptibility of neurons within various brain structures has remained elusive. Microglia, which are the brain's resident macrophages, have emerged as important players in neurodegeneration. Nevertheless, few studies have examined their implication in HD.Methods: To provide novel insights, we investigated the maturation and dysfunction of striatal microglia using the R6/2 mouse model of HD. This transgenic model, which presents with 120+/-5 CAG repeats, displays progressive motor deficits beginning at 6 weeks of age, with full incapacitation by 13 weeks. We studied microglial morphology, phagocytic capacity, and synaptic contacts in the striatum of R6/2 versus wild-type (WT) littermates at 3, 10 and 13 weeks of age, using a combination of light and transmission electron microscopy. We also reconstructed dendrites and determined synaptic density within the striatum of R6/2 and WT littermates, at nanoscale resolution using focused ion beam-scanning electron microscopy.Results: At 3 weeks of age, prior to any known motor deficits, light microscopy studies revealed that microglia in R6/2 animals displayed a mature morphological phenotype, not reached by microglia in WT animals until 7-10 weeks of age. Microglia from R6/2 mice across all ages investigated also demonstrated increased phagocytosis, as revealed by light microscopy and transmission electron microscopy. Furthermore, microglial processes from 10-week old R6/2 mice made fewer contacts with synaptic structures than those of 3-week old R6/2 mice and age-matched WT littermates. While synaptic density was not affected by genotype at 3 weeks of age, it only increased with maturation in WT mice between 3 and 10 weeks of age. The location of synapses was lastly modified from targeting dendritic spines to trunks at 3 and 10 weeks of age in R6/2 mice versus WT controls.Conclusions: These findings suggest that microglia may play an intimate role in synaptic alteration and loss during HD pathogenesis.