Accurate diagnosis of subtypes of transverse sinus (TS) hypoplasia requires more expensive methods like magnetic resonance (MR) imaging. We hypothesized ultrasound findings of the internal jugular vein (IJV) can be surrogate indicators for diagnosis of TS hypoplasia. MR images were reviewed in 131 subjects to evaluate TS diameter and the location and degree of venous flow stenosis and obstruction. Ultrasound parameters including the cross-sectional lumen area (CSA), time-average-mean velocity (TAMV), and flow volume (FV) at each IJV segment were also evaluated. Sixty-nine subjects had TS hypoplasia based on MRV criteria, of which 39 TS hypoplasia were considered a subtype of TS hypoplasia, which is secondary to the downstream venous compression/stenosis or left brachiocephalic vein. In the ultrasound study, the CSA of the IJV ipsilateral to TS hypoplasia was significantly smaller. Further, a contralateral/ipsilateral IJV CSA ratio >1.55 provided good sensitivity, specificity, and positive predictive value for discriminating TS hypoplasia.