IntroductionMeasuring Huntingtin (Htt) protein in peripheral cells represents an essential step in biomarker discovery for Huntington’s Disease (HD), however to date, investigations into the salivary expression of Htt has been lacking.MethodIn the current study, we quantified total Htt (tHtt) and mutant Htt (mHtt) protein in matched blood and saliva samples using single molecule counting (SMC) immunoassays: 2B7-D7F7 (tHtt) and 2B7-MW1 (mHtt). Matched samples, and clinical data, were collected from 95 subjects: n=19 manifest HD, n=34 premanifest HD (PM), and n=42 normal controls (NC). ResultsTotal Htt and mHtt levels were not correlated in blood and saliva. Plasma tHtt was significantly associated with age, and participant sex; whereas salivary mHtt was significantly correlated with age, CAG repeat length and CAP score. Plasma and salivary tHtt did not differ across cohorts. Salivary and plasma mHtt were significantly increased in PM compared to NC; salivary mHtt was also significantly increased in HD compared to NC. Only salivary tHtt and mHtt were significantly correlated with clinical measures.Conclusions Salivary Htt is uniquely associated with clinical measures of HD and offers significant promise as a relevant, non-invasive HD biomarker. Its use could be immediately implemented into both translational and clinical research applications.