Reliable markers measuring disease progression in Huntington's disease (HD), before and after disease manifestation, may guide a therapy aimed at slowing or halting disease progression. Quantitative electroencephalography (qEEG) may provide a quantification method for possible (sub) cortical dysfunction occurring prior to or concomitant with motor or cognitive disturbances observed in HD. In this pilot study we construct an automatic classifier distinguishing healthy controls from HD gene carriers using qEEG and derive qEEG features that correlate with clinical markers known to change with disease progression in HD, with the aim of exploring biomarker potential. We included twenty-six HD gene carriers (49.7 +/- 8.5 years) and 25 healthy controls (52.7 +/- 8.7 years). EEG was recorded for three minutes with subjects at rest. An EEG index was created by applying statistical pattern recognition to a large set of EEG features, which was subsequently tested using 10-fold cross-validation. The index resulted in a continuous variable ranging from 0 to 1: a low value indicating a state close to normal and a high value pointing to HD. qEEG features that correlate specifically with commonly used clinical markers in HD research were derived. The classification index had a specificity of 83%, a sensitivity of 83% and an accuracy of 83%. The area under the curve of the receiver operator characteristic curve was 0.9. qEEG analysis on subsets of electrophysiological features resulted in two highly significant correlations with clinical scores. The results of this pilot study suggest that qEEG may serve as a biomarker in HD. The indices correlating with modalities changing with the progression of the disease may lead to tools based on qEEG that help monitor efficacy in intervention studies.