Purpose Transcranial sonography (TCS) magnetic resonance (MR) fusion imaging and digital image analysis are useful tools for the evaluation of various brain pathologies. This study aimed to compare the echogenicity of predefined brain structures in Huntington's disease (HD) patients and healthy controls by TCS- MR fusion imaging using Virtual Navigator and digitized image analysis. Materials and Methods The echogenicity of the caudate nucleus ( CN), substantia nigra (SN), lentiform nucleus (LN), insula, and brainstem raphe (BR) evaluated by TCS-MR fusion imaging using digitized image analysis was compared between 21 HD patients and 23 healthy controls. The cutoff values of echogenicity indices for the CN, LN, insula, and BR with optimal sensitivity and specificity were calculated using receiver operating characteristic analysis. Results The mean echogenicity indices for the CN (67.0 +/- 22.6 vs. 37.9 +/- 7.6, p < 0.0001), LN (110.7 +/- 23.6 vs. 59.7 +/- 11.1, p < 0.0001), and insula ( 121.7 +/- 39.1 vs. 70.8 +/- 23.0, p < 0.0001) were significantly higher in HD patients than in healthy controls. In contrast, BR echogenicity (24.8 +/- 5.3 vs. 30.1 +/- 5.3, p < 0.001) was lower in HD patients than in healthy controls. The area under the curve was 90.9 %, 95.5 %, 84.1 %, and 81.8 % for the CN, LN, insula, and BR, respectively. The sensitivity and specificity were 86 % and 96 %, respectively, for the CN and 90 % and 100 %, respectively, for the LN. Conclusion Increased CN, LN, and insula echogenicity and decreased BR echogenicity are typical findings in HD patients. The high sensitivity and specificity of the CN and LN hyperechogenicity in TCS-MR fusion imaging make them promising diagnostic markers for HD.