Myotonic dystrophies (DMs) are clinically similar but distinct multisystemic diseases related to different repeat expansion mutations. CNS involvement is one important aspect of both, myotonic dystrophy type 1 and type 2 (DM1, DM2). Transcran ial sonography (TCS) has become a reliable diagnostic tool in the evaluation of several CNS disorders. The aim of this study was to evaluate TCS-findings in DM-patients in correlation with their clinical status. Thirty-one DM-patients (DM1 = 17; DM2 = 14) were examined clinically and sonographically by independent physicians. Echogenicities of basal ganglia and mesencephalic regions were assessed according to the examination protocol for extrapyramidal disorders using a Toshiba Aplio(®) XG ultrasound system. TCS abnormalities were correlated to clinical findings and secondly compared to 31 controls. Ventricle diameters were additionally compared to 3T-MRI volumetry. Nine patients (29 %) showed hyperechogenicity of substantia nigra. Mesencephalic raphe was hypoechogenic in nine (29 %) DM-patients and was more frequently in DM1 patients (p = 0.021). Width of third ventricle was significantly larger in the patient group (p = 0.021) and correlated with MRI-based volumetry (R (2) = 0.756). Pathological raphe signal was observed mainly in patients suffering from daytime sleepiness (sensitivity = 42.1 %, specificity = 88.9 %, p = 0,044), while alterations did not correlate with symptoms of depression. As a novel finding, a relation between mesencephalic raphe echogenicity and excessive daytime sleepiness could be identified in our DM-patients. An alteration of serotonergic raphe structures might be involved in the pathogenesis of hypersomnia in DM. TCS allows for measurement of third ventricle enlargement as a feasible bedside test.