Huntington’s disease (HD) is a fatal neurodegenerative disorder known for thirty years to be caused by an aberrant expansion of CAG repeats in the HTT gene. Still, no specific biomarkers are routinely applied in the clinical management of patients. The retina is the most accessible area of the CNS system that enables noninvasive monitoring of HD mutation carriers, but we need first to determine how retinal alterations correlate with those of inner brain areas. To this aim, we analyzed the transgenic R6/1 and the knockin zQ175 mouse strains using optical coherence tomography (OCT), gene expression analysis (RNA-seq, RT-qPCR) and immunohistochemistry assays.Symptomatic R6/1 mice showed abnormal retinal fundus and layer thinning, together with transcriptional dysregulation (differential expression and splicing) as extensive as the striatum, the most affected brain area in HD. There was an early dramatic downregulation of cone and rod photoreceptor markers followed by a late upregulation of gliosis markers. These two relevant periods in the progression of pathology was better resolved in the slow progressive zQ175 strain: the photoreceptor degeneration was highly prominent after 12 weeks-old and the neuroinflammation after 32 weeks. Immunostaining patterns of selected markers and additional transcriptomics analyses confirmed and expanded these findings. Other retinal neuronal markers were less altered, showing a similar degree of downregulation as the examined striatal neuronal markers. In conclusion, the HD mouse retina may provide important insights regarding HD-associated neurodegeneration and neuroinflammation.This research is financed by PI19/00125, CNS22/136169, PI23/01858, (ISCIII, MICIN, FEDER, NextGenerationEU), 2021-0406, 2022-0338 (ISABIAL), Fundación Navarro-Tripodi.