Huntington disease (HD) is a neurodegenerative disease caused by a trinucleotide repeat expansion in the HTT gene encoding an elongated polyglutamine tract in the huntingtin (HTT) protein. The use of biomarkers has become a major component in preclinical studies focusing on HTT lowering strategies. Quantification of soluble mutant HTT (mHTT) in cerebrospinal fluid (CSF) has served as a pharmacodynamic readout and as potential disease progression biomarker. However, development of future assays for HTT measurement from other biofluids, such as blood, will facilitate the access to human samples since CSF collection is an invasive outpatient procedure. Brain cells, in particular neurons, secrete extracellular vesicles (EVs) that cross the blood-brain barrier and circulate in blood. Importantly, EVs have been identified to be involved in HTT export from cells to the extracellular space. However, it is unknow which vesicle subtype correlates better with HD progression. Our work investigates the potential of EVs as non-invasive sources of clinical biomarkers in liquid biopsies. We developed an optimized ultracentrifugation protocol for the purification of ectosomes and exosomes from human samples and plasma of humanized HD mouse models. Ectosomes are larger vesicles that bud from the plasma membrane of cells, whereas exosomes originate from multivesicular bodies and are afterwards released to the extracellular space. Consistent with previous published data in other model systems, ectosomes isolated from plasma of the Hu97/18 mouse model contain both wild-type (wt) and mHTT in higher levels than in exosomes. Similar results were observed in media from HD induced pluripotent stem cells (iPSCs)-differentiated neurons and in Hu97/18 primary neuronal cultures. Interestingly, we also found higher levels of HTT transcripts in this EV subtype. We further demonstrate that initial storage of the samples using a slow freezing protocol preserves HTT and EV protein marker levels, highlighting the importance of sample preparation for EV isolation and analysis. Our results also show that plasma contains vesicles originated from neuronal cells that can be isolated using neuron-specific markers, such as ATPase Na+/K+ transporting subunit alpha 3 (ATP1A3), allowing the evaluation of HTT levels in the brain through vesicles circulating in the blood. Overall, our results demonstrate that HTT protein measurement from EVs isolated from blood can be a potential less-invasive disease biomarker. We also demonstrate that EVs subtypes contain different HTT protein and RNA levels, important for the development of consistent and reliable biomarkers. Further characterization of neuron-specific EVs content from patient-derived biofluids will lead to the development of novel clinical biomarkers and for evaluation of therapeutic strategies.